The big stuff seems like a no-brainer, that just has to go in totes/tubs since it is difficult to organize. The small stuff is more of a challenge, and here is my solution.
I use a padded double rifle case that is now discontinued, but there are many versions of this type of case out there. The key factor for me is external pouches and/or molle webbing so you can attach your own pouches. Examples:
The 42" Double Rifle Case: Reliable and secure transport for two rifles. Perfect for travel and storage. MOLLE/PALS Compatible.
condoroutdoor.com
This 2nd generation Savior Equipment Urban Warfare Double Rifle Case was designed with all the feedback they got from you. The Urban Warfare Case gives...
www.midwayusa.com
The G.P.S. Double Rifle Case is an ultra-high performance tactical rifle case which is built to accommodate a variety of rifles and shotguns. It also...
www.midwayusa.com
I am able to keep all the small items like magazines, ammo, tools, etc. in various external pouches on the rifle case, and access them directly. The most important pouch ended up being this one with the internal organization:
https://specops.us/op-order-pouch-cyb.html It's somewhat unique, and thats where I keep all the smallest items like hex wrenches, pens, picks, usb cable, etc. The other pouches size/design aren't as important because I'm throwing mags/pellets/FX chrony in them.
This system means the rifle case has most of the support items, excluding shooting bags and air tank.