My personal druthers:
I generally leave the ammo in whatever it came in until just before I load mags. Basically I am lazy, but also if I have a problem with the ammo, I know right away which other ammo came with it.
I would not mix ammo from different manufacturers, or even from the same manufacturer if it was different lines (e.g. 115gr FMJ and 115gr HP) because I want as much consistency as possible - different ammo gives somewhat different points of impact. And again, if I find a type of ammo that seems to cause misbehavior in my gun, it is a lot easier to separate if it is still in separate containers.
If I did empty ammo from its original containers, it would go into a bigger container, usually a surplus ammo can, like 10mmillie commented.
As for reloads, usually used the aftermarket plastic boxes for load development, but once I had something I liked, mass amounts went straight into the ammo cans. The only thing more awesome than a .30 cal ammo can full of bright shiny reloaded ammo is a .50 cal ammo can full of bright shiny reloaded ammo.

Of course the .50 cal cans require a little more muscle to tote around when they are full, but the awesomeness makes up for it.