i got FOMM to try make mod managing easier, and everytime i try to run it i get this warning "Unable to get write permission for fallout's installation directory. Please read the 'Readme - fomm.txt' file found in the fomm subfolder of your FOMM installation."

What does it mean and how do i fix it??

And i don't know if it's related to this but every time i load fallout and go the data folder to check/uncheck mod files, as soon as i check the mods i want to play and close the dialogue box, it unchecks all the mods i selected

To me, it sounds pretty straight forward. Did you read the Readme and follow its instructions explicitly? I'd start with that. Chances are its installed incorrectly (probably in the wrong folder or without its needed support files).

Have a read of http://www.gamesas.com/index.php?/topic/1117798-help-with-modding/, which is just down from this one. The OP has the same problem and MadCat (post #2) has suggested a way to fix it.

reinstalled fallout 3 into a folder outside the program files folder, ffom works better now and allows me to sheck/uncheck files.

However, in the data option on the fallout 3 launcher it still unchecks all my files, and now i am getting ctd's every time i try to start a new game.

I am running all of the DLC's and robert's male body replacer v3

If you're using FOMM, or FOSE, you don't need the launcher. Just use the box within FOMM, the one at the top.
If you have FOSE installed it'll say "Launch FOSE." Or, use the fose_loader.exe (create a shortcut to it) to launch the game instead.
The launcher doesn't work well with mods.