You can organize gameplay mods however you want in the mods folder without any problems usually, some mod makers recommend that you just put their mods in one folder in the mods folder and not any further sub folder, that's mostly for heavy script mods like MCCC. You also can't separate the .script file with the corresponding .package file.
I have separate folders sorted by creator, and I also have one folder that I call "No-Mods" which are mods that disable things from the game, which is useful because mods like that tend to break with patches.
