Large rubbermaid tote that contains a bunch of gallon ziplock bags that are labeled with the gun/caliber/etc. This is where they are stored. I have a range bag with a 10 slot mag pouch from Midway for taking to training.
what about 5.11's Ammo Mule bag? inexpensive ( $24 USD) and fits many packs and bags. https://www.511tactical.com/all-hazards-ammo-mule.html
My rifle case has magazine pockets on the outside. Other rifle and pistol mags go loose in my range bag or in the magazine loops in my soft-sided pistol cases. For storage I stack rifle mags in my gun safe or in ammo cans. Pistol mags go in the pistol cases or range bags.
I need more mags so I can buy something cool to put them in. Currently I don’t have enough mags to worry about it. When I go to the range I generally have my CCW and a rifle or .22. Just depends on who I’m with. I’m a shoot what I have on me kinda guy.