Sorry, after I re-read my response, it’s not as clear as I originally thought. When I said “they will not be eligible to move in noncombat movement either way”, I meant whether they attack or move away (having decided not to ignore the sub), not whether they attack or ingore the sub. Of course, if they ignore the sub they can do anything that they want. I’ll try again:
The presence of an enemy sub in your sea zone at the beginning of your turn doesn’t necessarily have any effect on your units there, since the sub doesn’t make the sea zone hostile. It depends on how you treat the sub:
Case A - Ignore It: You can pretend that it isn’t there if you wish, and it will have no effect.
Case B - Attack It: You can attack it, in which case all of your units in the sea zone must either attack the sub or move away in combat movement. They will not be eligible to move in noncombat movement either way, since they will have either moved in combat movement or participated in combat. Any transports will be able to load units before combat moving, assuming they are participating in an immediate amphibious assault.
I hope this clears things up.