I have no doubt that the Germans would need to replace the Hetmanate and Skoropadsky if they prevailed in the First World War - the regime was intensely destabilizing and led to the need for a large number of occupation troops in the countrysides to combat Bolsheviks and independent minded peasants who did not want to hand over their grain harvests. As
@Catspoke points out, the Germans are going need to provide some semblance of local government/autonomy to their new puppet states because the costs of direct occupation for the triumphant Reich are going to be extraordinary and they need all the hands they can get back in Germany to assist in the rebuilding of the economy and stabilization (particularly if victory comes in 1918)...
For this reason too, I have always doubted the argument that a German victory in the First World War is going to lead to an automatic White Victory in the RCW. Germany will be facing a kaleidoscope of factions in the former Russian Empire, all of which are united in their deathly hatred for the Reich (Whites and Reds). Those who can be made out to be "German puppets" dependent on the Reich for supplies will only be shooting themselves in the foot, and besides I am fairly sure a majority of the White leadership excepting some like Ataman Krasnov were unwilling to cooperate with the Reich given their death struggle for the last three years with Germany and their blaming on Germany for both the Bolsheviks and the fall of the Tsar. Even besides this, German material support could make some difference but not enough to change the contradictions that contributed directly to a White defeat (particularly the Volunteer Army of Southern Russia) such as lack of grassroots support given the lived experience of the peasantry with returning landholders despite promulcations to the contrary. It's certainly conceivable in some way that the Whites are able to claim a victory in this scenario, but I don't think the odds favor it and I view it as kind of an alternate history trope that betrays a lack of understanding of the dynamics of the Russian Civil War. It just assumes that "Big Monarchist Power" will fund "Russian monarchist movement" and lead to victory or something without interrogating the complexities of Russo-German co-operation, the infirmities of all of the regional White movements when it came to projecting power, the relative strength of the Red Army in this period, etc. I've even seen the argument that
Germany will for some reason decide to launch a massive offensive into Russia to crush the Bolsheviks, which I think is pretty silly.. They are in absolutely no position to do this by any metric and anyone in the Ober-Ost petitioning for a doubling or tripling the occupation territories in the East including some of the largest cities in Russia in the name of some vague polemics against Bolshevism would be laughed off. The stomach did not exist for a Hunger-Plan in the East either, despite some of the inclinations of the most virulent army nationalists like Ludendorff. I think Germany would try and secure a swathe of the East and move down into the Caucasus to guarantee the flow of oil in the region, but remain largely defensively postured to hold their (relatively) shaky hegemony. I'm of the opinion that the Reds will still triumph in the Russian Civil War regardless of a Central Powers victory late in 1918 .