There are a few steps that should be followed in order to set up a new mod folder. Please note, this doesn't mean you have to run the game installer a second time round.
Here is how you set up an additional mod folder (borrowed from the SF2NA Expansion pack install instructions):
- Open your SF2 Installation directory and make a copy of your preferred SF2 .exe file and its corresponding .ini file. Rename the copied .exe and .ini files to whatever unique name you prefer.
- Run the newly copied and renamed .EXE file, then exit back out to the Windows desktop after navigating through a few menus. A custom Mod Folder for your "[YourModFolder]" install will have been created in one of these locations:
Windows XP: \Documents and Settings\[username]\My Documents\ThirdWire\[YourModFolder]
Windows Vista: \Users\[username]\Saved Games\ThirdWire\[YourModFolder]
Windows 7: \Users\[username]\Saved Games\ThirdWire\[YourModFolder]
...where [YourModFolder] matches the name of the copied .EXE file that you created. You will install the downloaded mod files to this new directory.
As others have mentioned, it's usually beneficial to keep conversion mods in separate install mod folders. The author of the mod will often have set up lots of parameters like available aircraft, ground objects, terrains, effects, available years etc. that are specific to the theatre / theme of the mods and when trying to combine two it might cause bugs.
See here:
https://combatace.com/forums/topic/100316-downloading-from-combatace-read-this/
Bonus tip... calling it shitty whilst asking for help won't get you far.