The preferred way of loading FMs with the latest version of SS2 (v2.4 and newer) is the built in FM loader/selector named "FMSel". To activate it, simply update your game with SS2tool, and select the "Shortcuts" option. The shortcut "SS2 Fan Mission Selector" will be created in your Start menu, inside the "System Shock 2" folder. 

If you want to activate it manually, use notepad to open cam_mod.ini file in your SS2 folder, and you should see the option right away:
; always start the FM Selector (if one is present)
;fm
Remove the semicolon before "fm":
; always start the FM Selector (if one is present)
fm
This manual change will start the FM selector first whenever you start the game.

Save and exit. To start FMSel now either click the shortcut or run SS2.exe (if you made the manual change). You will be prompted about creating the FMs folder, choose yes, and exit. Now you should have a FMs folder inside your SS2 folder. If you want to install a FM, simply extract it into an appropriately named folder and move it into the FMs folder. Remember, each FM must reside within its own folder. Start FMSel again and you should be able to doubleclick the FM and start it up.



You can also create a folder where all the FM zip files will be stored (NOT in the FMs folder though), point FMSel to it (the option is under the gear icon in the lower middle part of the window) and FMSel will extract the FMs for you when you double click them.

Also do note that most FMs will come up with outdated installation instructions, do not follow them, especially if they are asking you to copy files directly into your SS2 folder - this is a very bad idea, and will mess up your SS2 install completely. If you already made this mistake, run SS2Tool in Perfect mode to clean up.