Copying non-steam FTL save to Steam
First, make sure you installed FTL on your computer (the one you want to move the save into).
In the "~/.local/share/FasterThanLight" directory, you should see 2 files:
- continue.save
- prof.save
Copy both of these files, and paste them into the "~/.local/share/FasterThanLight" on your new computer. If there are no files there, than that probably means that you simply haven't unlocked anything on that copy of FTL; simply replace any files there, or add them in if there are currently none.
If you are not moving the saves between computers, then don't do anything. Steam uses the same directory for saves as the non-Steam version, so you can simply click "Play" in Steam, and keep your saves.