Welcome aborad Swordfish12!!
The games been out for over 4 and a half years and we are still learning new things about it too.
The abbreviation of JSGME is for Jones Soft Generic Mod Enabler. It's a tool once downloaded and correctly loaded into your games root folder, that will keep track of the various mods you "activate" through its use. You use it before starting the game to change the game files with the mods chosen. Most, if not all mods have their files put together so they are "compatible" with JSGME and will go into the game seamlessly. One word of caution, loading the game full of mods can have detrimental effects if the mods overwrite each other in a way that takes away important files one needs. You need to know whether the mods are "compatible" with each other before taking the "all but the kitchen sink" approach to adding many mods to the game.
As a new player, I'd learn the game first before adding some of the mods through JSGME. The game offers many different ways to play. Depending on which "version" you have, you can play as an American or German Captain with either automatic targeting or manual targeting. Or, pick and choose the amount of difficulty you prefer.
Make sure your game is patched to the highest level. Depending on how or where you bought the game you're either using one of the first release CD versions that may only show the version of 1.0 in the bottom right corner of the "main" game menu screen. Or, you've bought a newer version (1.5 is the latest) found in the "Gold Edition" or you have the "U-Boat Missions Add on" which also has the 1.5 version. The "Add on" patches the original game 1.0 version and brings it up to date as much as the game producer allows. The point is, patch your game (if necessary) to the highest level to get the most out of it. Another version only patches the game to 1.4 (without the German involvement). There are fewer mods found for this version, even though there were plenty for the 1.4 version in it's day. Modders simply didn't want to evolve their mod with the 1.4 version after the 1.5 version (with the German side added) came along.
I think I'd spend some time at this post found
HERE. It's the "Sh4 Popular Mods, Tools, Technical advice and Tactical Tips" thread that will explain most of the abbreviations you don't know, and provide more knowledge than what you really want to know about the game.