Yes, definitely follow the instructions from the content creator. Some script / process mods conflict and most responsible creators (like those on MTS) will make note of the files being modified and what they might conflict with.
I also like to install my mods (by dropping them into the mods folder, which I have subfolders for mod type listed) in small batches, and running the game between installations, just to make sure everything is kosher - because it sucks when you load in 20-30 files only to find that you have a bad apple somewhere and your game won't launch.
