I don't think the boxes you're talking about will show up if you're using manual targeting in realism settings. The mod that I linked to will just show you where the vulnerable spots are at all times in the recognition manual, but you won't be able to select them.

i havnt seen those boxes once. :hulk:

Here are some screen shots of an attack run showing the recognition manual without and with the targeting boxes. The AOB changed from 84 to 86 and distance increased. Yes, I was driving backwards for reasons that are... uh... classified...

http://gollan.pwaresearch.com/p/C3_Attack_1.jpg
http://gollan.pwaresearch.com/p/C3_Attack_2.jpg

As far as I can say (and I'm not an expert): you have to be within 1000 m to target, the AOB should close to 90 degrees and gyroangle of torpedo must be between 0-15 degrees or 345-0 degrees (for bow tubes of course). As far these conditions are met targeting boxes should show.