I'll try to keep it short. First, I've been fishing a long time, so, like many of you, I have hundreds of everything, so trying to keep the stuff semi-organized is all I can hope for.
1. I have a large 6' X 4' cabinet (I need another lol) in the fishing lab that holds about a dozen plastic shoe boxes and another dozen 25 gallon plastic bins. In those plastic bins, I keep the back up plastics. There is also a large peg board with a few dozen hooks that hold back-up hard baits, spoons and assorted other plastics. In each of the boxes I sort baits by type - craws, finesse worms, stick baits, terminal tackle, jigs, spinnerbaits and so on. This is the back up stuff.
2. I keep around 15 or so 3700 boxes on my boat along with a large catch-all box that lives under another hatch. The 3700's are filled with baits depending on time of year and where I'm fishing. I keep most of my plastics in 3700 boxes on the boat (worms, craws, creatures, etc) each separated by type. I also keep separate boxes for hard baits by type and/or diving depth -- shallow diving cranks, lipless, mid-depth, deep divers, topwaters, etc.
3. I cycle through the boxes each season (I fish all year), swapping boxes in and out depending on time of year. The other 40 or so 3600 & 3700 boxes are in the basement cabinet with the other stuff mentioned above.
This system works for me and may not work for everyone. When I get low on an item I can go to the cabinet and refill the 3700 with the depleted bait(s). Each winter, I reorganize and sort items (takes a long time) and order what is out or running low.
*I also keep about 4 or 5 spare empty 3700 boxes (fits in my tackle bag) in the fishing room for when I go on other's boats. I fish with friends and rather than bring an entire box of lipless baits, square bills, craws, or worms, I can consolidate 3 boxes into 1 box so I don't have to bring 10 boxes along. Having the back up empty boxes saves me a lot of time. I can pack for a trip in under an hour versus if I didn't have empty boxes sitting there. All you have to do is sort through and drop them in the empty box. Much easier.
I tried to keep it short. Apologies for the novel.