1) If I want to use identity authentication, is there a reason not to use
MVC template? Or is there a reason to use empty template? MVC template
also provides bootstrap.
Identity authentication, MVC template and bootstrap are not really related.
If you create new MVC 5 application, AccountController is created for you. You can use that AccountController as starting point.
If you want, you can delete the AccountController and create one yourself, but it is a lot of work.
2) I have a database created, I want to have a DB first development. If I
use the MVC template, the database for credentials will be created
under the project folder. How can I merge the two database or I should
just use two databases?
You do not need two databases - you can place Identity tables and your custom tables in same database.
Start with Identity - let it creates database and its required tables. Then you can add custom tables to that Identity database.
Or
If you already have database with connection string, you can change the Identity connection name at the following place. Identity will create its tables inside that existing database.
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