I've found modding SH3 both a pain in the butt and a very rewarding learning experience. When I first started playing the game I was on stock for two weeks before GWX was strapped on. I was happy with that but as I browsed these very forums I discovered a whole new world just waiting to be created in my little SH3 'bubble'. Of course, the little things like a few skins and sounds didn't really cause any issues but as I found things like Racerboys SH4 Effects and new UI mods the situation went a little awry. Certain features stoppped working or caused stability issues due to the way whole files are overwritten by JSGME, so I needed a new approach.
That's when I discovered Winmerge (google it), a great tool for comparing text files (.cfg, .ini, etc) side by side and copying single lines or whole sections over to the other, making a backup automatically in the process. Through a very nervous and confusing period I managed to get myself a stable install with everything working how it should. Of course, depending on the mod there may be a few more complicated steps to mating your favorite addons into the game and eventually you will have to get down and dirty with Silent 3ditor but as long as you're prepared to take your time and do extensive testing, it doesn't take long before you start to learn filestructures and the particular section of a file or folder that may be causing an issue.
Before SH3 I'd probably done a few basic edits to my games but on this occasion it became a labor of love that has taught me a lot and given me my own personal flavor of the U-Boat war, so time well spent I think. Also, be prepared to read through from page 1 the entire thread relating to a mod, there'll normally be someone who has experienced an issue that you may run into or has provided good info on how to get that mod working with another. Most big mod authors will also strive to provide fixes or patches that enable compatibility so be sure to read those readme's before diving in.
If you just want to stick them in JSGME and have everything working you're going to be somewhat limited in your choices, but put in the time and effort and you, like me, will be greatly rewarded.
