Making a DIY Courier / Messenger bag

I remember that freightbaggage backpacks used to come with external flaps like postie bags, but they have now been redesigned. I'd like to ask to you bagmakers, I would have thought that external flaps prevent water from seeping under the flap and protect the external pockets more that internal flaps (which seal the main compartment very well though). Since I had water seeping in through the side stitch where the floating liner is attached to the shell I would like to have some way of getting the flap to cover the area to protect it! Mind you, the seepage only happened because the exterior cordura was totally soaked.

Not entirely sure what you are getting at - is this an extra top flap?
Or just raised sides (like Scott's Grobags?)
Also the whole point with a floating liner is that it is only attached around the opening rim of the bag - otherwise as you say water will wick up through the threads and into the bag. Due to the positioning of the flap edges (where the inner is attached) when they are folded over - there shouldnt ever be any part of it where it could get through....

Perhaps some pics/links to examples might help?