Something I learned from ancient SLR (film!) days - if your lens is anything longer than 2 or 3 inches, which is typical of all of today's zooms, do NOT lay it attached to the body with battery down, because if your bag is forced to be placed down with "rude" force or a weight accidentally is applied downwards whilst it is on a hard surface, you're putting unacceptable stress on the lens mount point due to the leverage on the longish lens. Worst case scenario, is, on the old bodies (as I found out!), the mirror box is sprung from the body ... which isn't a happy day for you! With today's monocoque bodies, this is less likely to happen, but misalignment is an everpresent fear, as the physics is the same!
With long lenses, there is no option really than to do it the "Lowepro" way - cradle the body left and right, and face the lens downwards BUT WITH WELL PADDED SUPPORT- this way, your zoom won't be extending on its own (if it tends to creep), and there won't be any undue stress on the lens mount area, even if the bag's to be bumped around a bit. You've got to appreciate that "travelling" from town to town, and "carrying" whilst on a shooting day are two completely different propositions - whilst shooting, I tend to re-arrange my 2-body bag once at my destination by fitting only essentials so that the two bodies slip in, with lens AND HOOD (if I need the hood on the particular lenses used) attached. Makes for less fiddling and safety against the odd bump when putting things away whilst grabbing a bite or a drink.
I advise you to (a) think through your movements, transport, etc., and (b) rehearse taking out AND PUTTING BACK everything for on-site confidence. At time of shooting, I would tend to avoid bags altogether, switching to a vest for the extra lens or two and filters.
Hope that helps!