I have yet to do quilting in more than one color thread. It would depend on how fussy your machine is about changing threads and will you use the same bobbin color throughout or change bobbin colors too?
I think I would be inclined to do my detail color quilting first then go back and do all my background quilting. I have a LA but I think the principal is still the same of the quilt being set up on the rack, it is just that you indicated you have a midarm so I don't know if turning the quilt is involved with your set up.