SH3Gen is an 'inteligence' program that gives you information on the position and the status of the enemy shipping. Have a look at this it might be usefull
http://www.global-explorer.de/
SH3Commander allows you to edit your crew, submarine details and patrol grid. You can promote your crew and hand over awards as well.
Now SH3 Commander and SH3Gen are totally stand alone programs and do not interact with SH3 (and GW, NYGM etc) you can use them without fear.
I use both SH3Commander and SH3Gen and I think they both are a must. Try them and see for yourself of course as this is just an opinion.