I have an old style Eclipse roller bag, has a divider in it for three long separate compartments, plus an additional smaller one on the side.
I load in my tanks on the bottom, one in each long compartment. Then guns so the barrels are sitting above the tank. Each long compartment can hold two full sized makers with barrels attached plus a tank and a hopper. I can also forego the tank and load in three markers. Usually has room to toss in extra pods or bits and pieces as well. It also has a covered flap for extra barrels if needed. Basic tools like allens, velocity adjusters, oil, etc go on the top flap.
The side compartment gets hoppers, spare tanks, or any other bits and pieces, along with the masks and lenses. Seal the bag up and pod packs get attached to the straps on the top of the bag.
The new Eclipse bags don't have the divider anymore, but still hold an insane amount of gear.
For protecting the marker, a heavy towel works great, plus you can use it to clean off paint between games.
On the higher end, Exalt makes some awesome soft sided cases and their hard cases are fantastic as well. The Inception ones that Exalt makes are also fantastic.
Just got my hand son one of the Push gearbags. I don't think they'd fit a pump or autococker, but they work great for everything else, even have a built in tech mat.