For 9mm and .22wmr I use a couple of combination lock boxes for my ammo. I don't take them out of the boxes tho. I keep forgetting to swing by Office Depot to pick up a couple more for my overflow. I got shit sitting on top of one of the boxes that has a mix of 9mm and .22WMR in it. Actually, I have a couple hundred rounds of .223/5.56 sitting on top of the box that has the majority of the .22WMR in it. I really gotta get that shit together.
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As for spare magazines, I have plenty of spares for everything except my Taurus G3 and Smif .22 Compact.