I got it to work. Noticed a enable game pad line in Skyrimprefini file. Had to go to the one in the mod organizer under the profile. Thank you thane for pointing me in the right direction.
I realize that there has to be a file that recognizes my game controller when i run SKSE without MO. Anyone have any idea what that might be? I am using a XBOXONE controller. I did not have any problems with it before MO. MO just does not recognize my controller. ANything i can do? i know i am being repetitive, but as long as the point is eing made right?