I need help playing the mods I downloaded. I dont Know how to get them to show up on the "MODS" section of the main menu. Can somebody help?

All you should need to do is find the games folder and then add mod and the mod name subfolder under that so:
Far Cry\Mods\[mod folder name]

wait do you mean to say i open the game and click mods on the main menu
or i go into the farcry folder and drag the mod icon into the mods folder??

Not in the game, find the actual folder and then put the mod files in there own folder with the mods name as the folder.
So it would be something like go to Far Cry folder then open or add a Mods folder in that directory. Then add a folder with the mods name you want to play under the Mods and make sure all the mods files are in that folder.
So it would look like Far Cry\Mods\Weapons Mod or Far Cry\Mods\Mutant Mod

Im having an issue too with getting a mod to work on far cry. I downloaded a mod called "Project Far Cry" and my problem is that i installed far cry off from steam and i notice theres no mod folder, so I need help