It isn't as major of a deal as it first seems. The computer will only send subs automatically if the sub is in port.....so, don't put it in port.
Play careful attention of when you receive subs as reinforcements. When you receive sub reinforcements, immediately put those subs in TFs.
When you "need" to put a sub into port because of damage, make sure that it is assigned to either a shipyard, pier or repair ship the same turn that you put the sub in port.
When you need to put a sub into port because of an upgrade, make sure the sub has damage first so that you can assign it to shipyard, pier, or repair ship the same turn you disband it into port. If the sub is undamaged, assign it to patrol around the base you are going to upgrade it in for awhile. If you set the speed to "fast" it will become damaged faster. As soon as it has 1 point of any type of damage, you can put it under repair. While it is under repair, it will upgrade. I usually like to insure it has either engine damage or 3-4 sys damage. 1 or 2 points of sys damage might get repair on it' way back to port and you will need to send it back out again.
Pay attention to when those repaired subs are fixed. As soon as they are fixed, put them in a TF and the computer will not be able to take control.
Check the sub list as mentioned every few turns and check to see if a sub or two slipped through.
If you follow these rules, you will have very little problems with the computer taking over your subs.
< Message edited by Charbroiled -- 10/18/2011 4:58:09 PM >
"When I said I would run, I meant 'away' ". - Orange