We put all the diapers, wipes, etc in ziploc bags and then we put those in the bottom of the stroller. We also had a change pad and some plastic bags under there. And, anything else we needed/valuables I kept in my bag (an over the shoulder bag).
We just put all the ziplocs in a cloth bag (the reusable grocery store bags) when we had to fold the stroller.
Truthfully, my diaper bag so quickly becomes a bottomless pit and is full of stuff that I wouldn't want to lose.
Someone I work with left his camcorder, digital camera and wallet in their diaper bag and it got stolen from hanging on the stroller.
Mind you, it was an expensive stroller and a REALLY nice (Kate Spade) diaper bag, so not to justify it, but it was kind of screaming out to be stolen.