I've fluctuated between swapping things around, and keeping electronics with each rocket. The way my fleet has developed, I tend to have a generalist rocket or two, and then several special projects in the works. The general fliers keep their electronics year round, while the special projects typically only fly once or twice before the electronics move to the next one.
When I first started flying with electronics, I tried to integrate them into small pods that could be swapped between avbays that just had several 29mm tubes. This ended up being a pain in the rear, and I converted my only rocket with the system to a conventional avbay. From there, I've mostly had one avbay with electronics for each rocket, although I have moved altimeters around to get various rockets up and ready.
I did come up with a really nice solution for easily swapping electronics between rockets while working on my second L3 attempt. I built a really compact avbay for a 75mm minimum diameter BALLS project this year, which managed to fit a Stratologger CF, EasyMini, and a Featherweight GPS into 2.5" of 75mm coupler once the GPS antenna was relocated. For my L3, I rewired it with wires going to connectors, and then put corresponding connectors and wires on the bulkheads and switches for my L3 and a 5.5" Nike Smoke I helped my dad build. Swapping the electronics around was pretty simple, and I'll probably keep the same spacing between the threaded rods on future large avbay designs to allow this sled to work with them.