I only use one color and I just dump them all over the bottom of boat

Looks like a Sharpie paint pen in white. Leaves a long lasting easy to read inscription. The paint pens work well on Gorilla Tape.

I keep all my plastics in their original packaging.

Then, I use those Jumbo 2.5 gallon ziplock bags to further separate and categorize them (have about fifty)

The most important plastics to keep separate are the Elaztec plastics (Zman and the Strike King Elaztec baits)
One bag for Zman worms, One bag for Zman Ned sized plastics, One bag for Zman creatures and frogs

Two bags for 6inch and under worms in clear water colors
Two for 6 inch and under worms for stained water colors
Two for 7 inch and over worms in clear water colors
Two for 7 inch and over worms in stained water coors
Two for craws in clear water colors
Two for craws in stained water colors
Two for grubs in clear water colors
Two for grubs in stained water colors
Two for shad and lighter colored flukes
Two for bluegill and darker colored flukes
One for lizards in clear water colors
etc, etc, etc

This all stays in the house and/or garage with all the clear water colors on one side of the room and all the stained water colors on the other side of the room. The night before I go fishing, I just take what I plan on using--definitely minimizes what tackle I have in the boat and/or the kayak. In hindsight, it would have been easier just to buy everything in black and blue, white, and Cali 420

I store my plastics in their original packaging, sorted by color, type, and a gallon ziplock bag.

OK, so what's wrong with taking plastics out of their original packaging and keeping them sorted (by color, etc) in the various compartments of a Plano box? Is there a "freshness" factor if you keep them in their original packaging? I go through the basics (flukes, senkos, brushhogs) fast enough that a full package of baits rarely last longer than a few months. I wouldn't do this with Power baits.