Such a basic question I'm almost embarrased to ask it but here goes -
I'm putting a multi color warp on my warping reel and some of the threads are odd numbered. I started my warp on the lower peg of my warping reel. Should the last odd numbered thread end on that same peg or on the upper peg?

If I understand you correctly - Depends on your total number of warp threads. If total is even you should end on the bottom peg. If odd end on the top peg. (And remember to catch that end loop in the rod when you put it through your cross.)