Seems like the best practice would be to keep the total load (rider, panniers, water, etc...) between the axles. Kind of like a truss, rather than cantilevered over the axles. If you can adjust for this and keep your bags far enough away to avoid any interference, that'd be the ideal I would shoot for.
Again, this is just my opinion and every one has one of those, so take what I say with a grain of salt, as it were...