R – If i use a separated ASP.NET Membership database how should i handle the relations to the user tables

This can depend on scale. If it's an enterprise solution with different apps sharing one membership source the answer is simple - separate them. There might also be performance reasons why you would want to separate this data from the rest of the app. Arguably these tables do not belong in a data warehouse for example.

The only thing the 2 databases solution doesn't give you is referential integrity. If you extend your membership tables to hold more application specific details about the user, and these tables need to link into the main database then you might want to keep them together. Otherwise you would need some sort of replication job maintaining this for you.

Why not do it the other way around? You can implement your own Membership provider for asp.net, that uses the model you want/need.

If the features you need aren't a complete match with the built-in asp.net membership implementation, you can just roll your own provider. If you will use just a couple features, you will have to implement just a couple methods (you don't have to fill implementation for all the methods). If you need more features than it supports, using the membership provider might get in your way.