deploy 2 database for single website

There should be no problem if you keep two databases for a given website. All you need is two databases deployed and a valid connection string pointing to them.

This can be done for some scenarios, like you want to store one type of data in DB1 and other type in DB2. All you would need is to place a code for picking the defined connection string for a particular scenario. (Though you need to pick why you need two DB's!)

Apart from this, the connection/deployment is same as what you do for one database.