i was hoping to find a bunch of creative alternative uses for the mostly unhelpful canon lens pouches, given the title
but since i'm here...
in general i use the pouches for at home storage, and when i'm out and about, my lenses are usually in a camera bag of one sort or another not in pouches. if your messenger bag is not specifically photo oriented (ie, no individual padded compartments for various pieces of equipment) i would suggest some lens wraps as the snuggest least bulky way to add a little protection to your gear. if it is a photo messenger bag, just leave the cases at home.