Merge with Playable Subs worked for me as well.
Just copy the payable subs and objects from Playable Subs into the campaign summary of Freeroam.
Modern subs seem to be a bit OP though, it would be nice to have some more difficulty when playing a Seawolf for example.
Also I found the main soviet ports to be protected by only 3 merchant ships twice. It would be more challenging if there would be warships and subs guarding the port.
Thanks for the mod, had hours of fun with it so far.