1. Prussia, basically covering the areas marked 'Mecklenburgisch-Vorpommersch', 'Märkisch' and '(Ober-)Sächsisch' and every German area east of there on
this map.
2. Unified Austria and Bavaria, including the southern Sudetenland and South Tyrol. So basically what's marked 'Bairisch' on that same map.
3. A West German Confederation, stretching out from Schleswig to at least the northern border of Switzerland, but possibly even incorporating all of German Switzerland. It shouldn't include the Netherlands however (as on the map I linked), or at least not the Low Franconian (i.e. Dutch) speaking area. An 1800 POD still allows for regional Low saxon dialicts in the north-eastern Netherlands to be prevalent enough to join that area to Germany linguistically (German can gradually replace Low Saxon just as well as Dutch did in OTL), but I doubt the region's inhabitant's would he happy. (They'd be less likely than the rather more culturally German Swiss people to accept becoming German.)
That third country is the trickiest one to form in any case, because it's basically "everything that's not Prussia or Austria-Bavaria". Yet you want three states that can really be called a 'Germany', and this is the way to make that happen. The West German Confederation would include catholics and protestants, and various Low, Middle, and High German dialects. It would have to be confederal or (decentralised) federal in order to function well, but that can be arranged.
The three countries described here would be able to keep each other in check. None would be able to dominate. It's pretty much a stable situation. This kind of thing
could have been implemented by Napoleon, which fits the c. 1800 POD for this...