Since you ask multiple questions, you may have to get multiple replies - or be asked follow-up questions to clarify your situation.
It's a pretty big leap from 11.3 to 12.1 I would not install the new system over the top of your old. Just doing an install of 12.1, you should still be able to run your existing setups with no changes - at least none that come to mind as far as GenData/GenPrint are concerned. So immediately after install (and with a path change) you should be able to test your previous runs against new runs.
The BIGGEST difference from 11. 3 to 12.1 is that you will be moving from the old Image Editor and separate tools up to the DMStudio managed model. This means you will need to create a workspace for Studio to manage. The workspace creation wizard will ask to import your resources into a workspace. Normally, I again suggest that you allow this to create a new table for your resources so that your old system continues to function as you find your way around in the new world.
I don't think the library layout changed between 11.3 and 12.1, but you probably still don't want to modify your existing setup until you know you have good output using 12.1. You will likely end up with more resources under library management after the fact than before.
The DMStudio wizard will create tables for you if you have the rights to do so. If not, then the page will offer for you to generate the DDLs to give to an DBA that can.
A lot of this should be documented either in the install guide or in the document that specifically addresses DMStudio.