I usually advocate for putting lenses in your bag mount-up: It's both a lot more convenient for shooting, and also puts lens hoods between any glass and the ground. (Also it means if you're not religious about putting lens caps on before changing lenses, everything's a lot better and cleaner that way, too. Rear caps are also much less likely than lens caps to come loose and do a little dance on the nearest optical element.
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And I *usually,* but not always, carry cameras with mounted lenses facing down in the bag. (That varies a lot depending on the camera/s and the bag: it's nice if the primary body/lens can have its own little nest, but I tend to wanting to use smaller bags that end up pretty tight. Lens-down saves a lot of bulk, though in bigger bags or if I were a bigger person, I'd worry less about that. I find that my way is a *lot* more convenient if you're mixing film and digital, too, but I always did it that way, before digital, anyway: I'd have a primary body, usually loaded with B&W and another with color or slower film or whatever combination made sense for the occasion. Now it's arranged a bit differently: now digital does many jobs and the second body is loaded with B&W for backup and when it has to be film.
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