@D.Sims I got your six.
All I can offer is my opinion, you’ll have to decide YOUR system.
I hate to say it, and most everyone HATES to hear it, but keeping an inventory, especially on an Excel spreadsheet, is almost a must, once you start getting deep into this. Double buying, unneeded panic buys, running out of stock, are ALL issues without having an easily updatable, accessible list. I highly recommend going through you entire stash, writing it down (makes it easier), then get a drink (or seven), and load them ALL into a spreadsheet. I run two, one for my small bottles, and one for my jugs. I “try” to track burn rate and trends, but it’s a work in progress.
I organize ALL my flavors first by MFG, then alphabetically therein. I’ve never had any other system that works. Ideally you’ve have racks for all of your working bottles (small). Racks are great, because they allow you to SEE all your flavors, and most are 5-7 tiers, so you can always see on each rack. Makes for easier use.
If space/money is at a premium, you can rack up whatever you use most, then keep clearly MFG labeled boxes for other bottles, so you can easily get to them in a hurry. You had mentioned gallon ziplock bags, which might be great for possible leakage, and reducing some smells, but it’s got to be hard to be constantly opening, closing them all the time.
You know HOW you mix, and how OFTEN you mix, and those two things will probably decide for you best.
Oh, and by the way, you had me at …