Welcome aboard. Bill's site explains SCU, and you can download it there:
http://www.subguru.com/downloads.html
Regarding crew areas, I would strongly recommend learning sonar, as you will be more competent than them. I usually set and fire my own torps as well. I have never bothered with TMA personally.
Creating missions, especially campaigns, is fun. I am just about to compile a few myself after a long time away. The SC manual gives you quite a good guide to this, and there is a file explaining how to create a campaign on Bill's site. Good luck!