I wouldn't bother with putting soft plastic lures into plastic boxes. Keep them in their original packages. Group similar lures together in gallon zip lock bags. Be mindful that the zip lock freezer bags are a heavier duty plastic than the regular zip lock bags. I wouldn't mess with the regular zip lock bags. Sometimes you will tear up the original packaging. Have some quart size zip lock freezer bags on hand and transfer baits into that bag. Take out your sharpie and be certain to label brand & color. Take the gallon zip locks and keep them in a cheap duffle bag. Myriads of different sizes of cheap duffle bags are available. Pick one that suits, be mindful that as your soft plastic assortment grows, you will probably need more than 2. 3 or 4 is a good number to start with and allows you some room for growth.
A few years ago, Walmart had cheap, wheeled, soft sided carry on size luggage on sale. The ones I found measured roughly 20" x 12" x 7". I bought 5. These stack easy in my Explorer and are easily bungeed down on the back deck of my boat when I fish by myself.
I've been doing this for a few years now. After you have been doing it for a few years, you will find that there isn't any perfect system. I try to have one or two carry ons for each season. Spring soft plastics - fall soft plastics and summer soft plastics. There is some overlap, but that don't matter. The point is to have a bag that you can grab and go and have enough options within that bag. Another option is to divide baits by water color, i.e. baits for clear water - stained water - dingy water - muddy water. Experiment with your secchi disc to figure out what these different water color titles mean where you live. By this I mean that what is considered clear water in Texas isn't the same thing as clear water in Missouri. Even in Missouri, Lake Ozark clear isn't the same thing as Table Rock clear and neither of those are the same as Bull Shoals clear ( which is mostly in Arkansas, I know)
Whatever soft plastic system you decide to employ, be sure and label it. Do not count on your memory because it will betray you at the worst possible time. I have went through several different labeling systems. I have found duct tape and permanent marking sharpies to be my current best system.
I hope this gives you an idea of how to sort your working assortment of soft plastics. How to sort your spare & extra soft plastics that you keep back in your fishing shed is a different topic.
Here is a hint for that storage issue. Dust, insects & mice are your enemies here. Go to Walmart and buy many plastic shoe boxes. I think that the ones with the attached lids are better than the ones with the separate lids. Buy several different colors of duct tape and label everything, trying to stay organized. For me, Berkley plastics are one color of duct tape, different brands of worms are sorted by length and type of tail and are another color. Baits that I have a lot of, like trick worms, get their own box (or 2). Lizards get a different label color than worms; same goes for tubes, craws, creature baits, swim baits, what have you.
If I have aided you in your soft plastic organization strategy or added to the confusion, then my work here is done. On another side note, once you have decided to take an afternoon and devote it to soft plastic organization, I find that several IPA's and a blasting stereo help. Bridgeports (out of Oregon), Boulevard Pop-up IPA (out of Kansas City), O'Dells (out of Fort Collins, Colorado) and Deschutes (another Oregon Brewery) are a few good IPA choices to start with. Don't get bent out of shape if you don't get done in one afternoon. There will be more afternoons and more IPA's. Tune wise, on the stereo, I have found that Bob Wills, Billie Holliday, George Thorogood, Dwight Yokum, Lynnard Skinnard, Count Basie & Bob Marley to all be good soft plastic sorting tune choices.
Oh, by the way, in your profile, it helps to know where you live. Guys who live more or less in your neighborhood will be more likely to respond.