Just watch your mods. RFB 2.0 and TMO stand alone. Do not mix and match them. Then, if you use Run Silent Run Deep (RSRD) for traffic make sure you use the correct mod file for RFB and TMO. Read the first post of each mod. Pick the one you like and stick with it as far as what will work that that mod and what will not. You can always run two installs of SH4 thus running both mods. You have two careers going though. Up to you. Most important is each mod does not conflict with other mod.
Yes, use JSGME for mod installation. Just the greatest tool for mods in the world.