Depending on the size and weight of your duffle bag, two low cost solutions that I've either tried or currently contemplating:

-Find you some old election campaign signs and put them in the bottom of your bag. Then use a cargo net to hold it down to your rack. Jandd and Ortleib both have rack duffles, but I think they use foam, and they incorporate velcro straps to anchor to the rack.

-Do what I did.