10) download + install JSGME
11) Run SHIII once
12) configure JSGME
13) install mods
14) install mods for SHIII Commander (like GWX combined skin pack)
15) remove the files in data/movies/backgrnd and data/movies/intro to skip the annoying intro movies
13) run SHIII through SHIII Commander
When your pc is not very up-to-date you can also install FSautostart to kill unneeded processes before running SHIII (commander)
Mods I use (and recommend

:
- GWX lite harbour traffic (if your computer is a little slow)
- torpedo damage final (for huge holes in ships after torpedo impact)
- racerboys sh4 effects for sh3 (for great effects)
- the real ping (for real ping

- racerboys hud (for easy manually targeting)
- exhaust smokes (you can find them for all u-boats in racerboys collection)
Good luck!