I collected some details on German Confederation plans for war in this period, from Monica Toft and Talbot Imlay's The Fog of Peace and War Planning:
1831: 'Roder told the Austrians that Prussia would fight only a defensive war, but in such a war would contribute 200,000 troops… He was instructed to offer Prussian troops to bolster both a right (northern) flank including the IX and X Corps, drawn from the smaller northern states, and a centre including the VII (Bavarian) Corps and the VIII Corps, the latter drawn from Wurttemberg and smaller southern states. Austrian troops would form the left (southern) flank on their own. Under such a mobilisation plan Prussians would dominate the federal army, and it would be difficult not to have a Prussian general as supreme commander.' 'By the time Roder left Vienna in early April 1831, he had to concede to the Austrians an even north-south split of command of any forces in Germany. In return, Metternich agreed not to push for the immediate selection of Archduke Charles as federal field marshal: at the time, it was widely assumed that Charles had enough votes in the federal diet to be elected commander.'
1832: 'A northern force would consist of 60-70,000 Prussians plus the X Corps; a central army, of 90,000 Prussians, the 30,000 Bavarians of VII Corps, and the VIII and IX Corps; and a southern army, of 150,000 Austrians… Austria accepted the terms of 3 December 1832 because the south German states had persisted in their refusal to be subordinated directly to Austria in the ultimate order of battle.'
'In a draft treaty concluded on 28 November 1840… The 1840 order of battle also favoured Austria more than its precursor of 1832, as Prussian negotiators conceded to the Austrians overall command of the Bavarian VII Corps and south German VIII Corps within a southern army on the Upper Rhine. Austria’s only concession was to agree to give the same two corps a measure of tactical autonomy… The south German rulers grudgingly accepted a German federal guarantee of Lombardy-Venetia but rejected the idea of serving under or depending upon the Austrians… [the Austrian general Heinrich von] Hess found that [the Prussian colonel] Radowitz had communicated his own version of the draft treaty of 28 November [to the South German states]… a north German army and a middle Rhine army, each under Prussian leadership, a south German army (including VII and VIII Corps) bolstered by more Prussian troops, and a separate Austrian army, thus giving Prussia control over all German forces except the Austrians. According to the agreement of 28 November, the northern and middle Rhine armies, indeed, were to be led and dominated by Prussians, but the VII and VIII corps were assigned to a single southern army under Austrian command and consisting primarily of Austrian troops... Frederick William IV sent another despatch to Vienna at the end of January 1841, calling for a revision of the November draft treaty to separate the south German VII and VIII Corps from the Austrian army on the Upper Rhine... in effect, to make the actual agreement conform to the false version Radowitz had explicated'
What I find interesting is that the King of Prussia wanted the Duke of Wellington as overall commander-in-chief:
Charles Greville's diary,
September 1, 1841: 'It seems clear that the Duke will hold no office. In June he wrote a letter to Peel urging all the reasons why he should not hold office, but expressing his readiness to do anything he might think most serviceable to his Government. Among other reasons he said that a war was not improbable in the unsettled state of European politics, and in the event of its breaking out he should most likely have to take the command of an allied army in Germany, thus exhibiting his own reliance on his moral and physical powers. I did not know (what I heard yesterday) that last year the King of Prussia sent to the Duke, through Lord William Russell, to know if he would take the command of the Forces of the German Confederation in the event of a war with France. He replied that he was the Queen of England's subject, and could take no command without her permission; but if that was obtained, he felt as able as ever, and as willing to command the King's army against France.'
Rory Muir's
Life of Wellington: 'A note by Greville’s first editor, Henry Reeve, states that this overture came a little earlier than Greville believed, in January 1841, and Wellington’s reply was dated 30 January 1841. So Wellington’s talk of needing to be free to command the allied armies in Germany in the event of war was neither as far fetched nor unreasonable as it might seem at first sight. (Greville Memoirs (ed Strachey & Fulford) 1 September 1841 vol 4 p 405. Wellington’s reply to Russell is in WP 2/73/178 and 179; Russell’s letter does not seem to be present. It is not quite clear from this reply what exactly the King of Prussia had proposed, but the docket on the copy, written by Wellington’s secretary, summarizes its contents as ‘The Duke ready to take command of the Confederation Armies in case of a War with France’).'
Queen Victoria's journal,
2 January 1841: 'Afterwards I talked with Ld Melbourne & Ld Clarendon, of the Duke of Wellington & his having so gallantly said, that in case of war, he would command the Confederate German Army, which had been offered to him, the other day, by the King of Prussia.'
Presumably this was as an alternative to Archduke Charles. However, if you've got two armies led by Prussia and only one by Austria (or even two Prussian, one South German and one Austrian), I don't see how you could legitimately deny Austria the overall command.
ED: Better details on the deployments, from Miroslav Sedivý's Crisis Among the Great Powers: The Concert of Europe and the Eastern Question.
‘an agreement was signed on 28 November 1840. According to the contract, the two Great Powers were obliged to defend the German Confederation, particularly the Rhineland. Prussia had nine army corps and was prepared to employ them all on the Rhine, and Austria promised to send all her forces which would not be in Italy in the same direction. The operational plan was largely based upon the one prepared in Potsdam. Three federal armies were to be created against France: (1) the army on the lower Rhine consisting of the 3rd, 7th and 8th Prussian and 10th Federal Corps and situated between Trier and Julich and operating either against France or Belgium, (2) the army on the central Rhine comprising the 4th, 5th and 6th Prussian and 9th Federal Corps deployed between Frankfurt and Wurzburg and destined for the defence of the territory between the Saar and Moselle or offensive operations against Metz and Champagne through Lorraine, (3) the army on the upper Rhine consisting of the 7th and 8th Federal Corps assuming a defensive position at the beginning of war and waiting for the arrival of three Austrian federal corps. On the Elbe three more Prussian corps [Guard, 1st and 2nd] were to form a reserve army. The goal of the German armies was to assume an initiative as soon as possible and launch an offensive since it would cause the faster unification of their forces. Since both Powers feared that Belgium would not maintain neutrality and would join France and that the latter would not observe the neutrality of Switzerland, it also was stipulated that Austria would establish an observation army of 30,000 soldiers to protect the federal frontier with Switzerland whereas Prussia would use her army on the lower Rhine against Belgium. They also counted on the Russian reserve army waiting on the Warta river; its deployment would be decided in compliance with the course of operations and merely in the case of need since its use was also regarded in Berlin and Vienna as a necessary evil.
The number of troops was not settled in the agreement but can be compiled from other sources: Prussia’s army was to offer for the three armies on the Rhine 94,200 men, 12,600 horses and 288 cannon, the reserve army on the Elbe would comprise 96,304 men and 13,200 horses. They were to be prepared for battle within six weeks. The Austrian army would increase its forces in Germany gradually and within 18 weeks it would be deployed in full in the number of 150,000 soldiers and 402 cannon, but a considerable part of this number would be prepared for fighting in southern Germany in a shorter period; the Italian army was to be reinforced up to 120,000 men by the troops from Hungary, Carniola and Illyria.’