Look up Import Records in the online help system. This is a powerful tool that can do a lot of different things for you.
In your case you can import your data from your two different files into a third file. You'll need to do this for each table in your file. You can script this is you want.
The one thing that I'd beware of are any serial number ID fields that function as Primary keys. You could easily get major data confusion since the values will likely no longer be unique once you've merged your data. You may need to implement a different primary key strategy to insure that this doesn't happen.
Set a field to auto-enter the current serial number field combined with a Hospital ID value to get something like 1234.1 for one hospital and 1234.2 for the other.
Yes, I had thought that - we use a specific site code in the UK for each hospital, there are 4 hospitals within the Trust I work each one starts something like FMP01, FMP02 etc, this is the first part of the unique identifier for each table (eg FMP01_PATIENT_00000001, FMP01_TUMOUR_0000001 etc) within the database so that i knew exactly where the record was generated.
I could always add an extra field in the master database for the serial numbers from the tables in the daughter databases... that should work with minimal additional work to the master database.
The thoughts are mulling well now ;-)