I've 2 sql server databases on two different remote servers. On the first day, these were both exaclty exactly the same. But with time, you will find alterations in both (different, tables, saved procs, sights, etc..).

How do you merge them together, and so i have one again - exactly the same Database both in places?

I'd take a look at Red Gates SQL Compare, whether it's a large schema, it is extremely helpful.