The first thing to do is to connect (relate) the two unconnected databases. Depending on how they're structured you may be able to view all the data you need from one file on a layout of the other simply by dragging fields onto the layout or by using portals. You may not need scripting. As well, even if you do script, the files , or tables contained in them, will need to be related. FM doesn't care if all tables are in the same file or in different files. If you're new to this, look for "Relationships" in the online help.
Ah, I didn't realize that FM didn't care if the tables were in separate files. Since I can relate fields in different databases, this becomes pretty easy. Thanks!!