I am very unfamilair with the G.E.C.K. and I am currently messing around with effects I am adding to clothes, and it seems that you can not reducing a non-combat skill, medicine in my case. Is there any way to add a -5 medicine to apparel? or any non combat skill for that matter?

You just need to make a new base effect. Go to the base effects section, find one of the ReduceXXX effects (like ReduceGuns) and change the ID to something like ReduceMedicine, and alter the value it affects to be Medicine.

Thank you sir or ma'am, you have been of much help to this G.E.C.K. novice.