I downloaded swarm and the cyborg zombies scene and i cant find them in game. WTF

Have you put the .rte folders into the root Cortex Command directory?
Where in game are you looking for them?

all of my scenes are in the base/scenes folder ive also tried just putting them in resources do they need to go into the missions scenes folder?. Ive looked in skirmish and campaign so im really stumped. the mods are swarm and cyborgzombies.

The .rte goes in the Cortex Command folder. Also make sure the folder opens to the Index file, and not another folder.
Here's a thread that might help: How to install mods.

i have plenty of mods on CC these two are just being weird

You need to put them in the same place as the other mods. This is the same place as the Cortex Command.exe file is.
They will appear in the same place you access the Tutorial, Maginot, Zombie Cave and Dummy Assault.

ok now they work i got confused because my other scebes would work if i placed them in the base.rte/scenes.rte folder but thank you