Try: cheat ssf sub
Should spawn the sub and make you control it.
Once we leave the seat though we do need the skill "explore the Depths" to get back navigate the sub.
I used the Admin Menu to give myself Creative mode.(Unlocks all quest skills)
After that I could control the sub at will.
cheat showmyadminmanager
You might want some mythos to power the sub:
cheat GFI MagicMarrow 500 0 0