Brainstorming here. Our current organization probably isn't the best way. For example, for helmets, we store them in a container. Then there is a gallon back for the first digit of each item number( bag for numbers that start with 1, another for 2, etc.). Then inside the gallon back, I have each different type of helmet in their own bags; some even by color. So to get a helmet, I have to open and close a container and 2-3 bags. Not the ideal way to do things.
So how do you do it? And not just for helmets, but for the rest of the minifig stuff (torsos, weapons, etc.)
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It's just a quick pull of the bin then, finding it, and closing the bin (I only keep full minifigs in bags). So I guess my key is to keep like parts (minifig-related or not) in completely sep bins to avoid the slowdown of verifying any variations when I pull.
The nice thing is as things sell, different items go into the bins - so little stays in the same bin forever. :-) You do have to be super careful with your data entry though, checking you have the right bin when you hit enter and ensuring all changes save (the green banner), because you will NEVER find something if you made a typo, lol). Though... I also add a last sighted date to my private notes. So if I'm moving something from one bin to another to make room for more of a specific item and I want to keep them together, that date has saved me twice, as I can view by date and see what bins I was mucking with that data entry day...
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Stick a tray number on them, and then the lot remark is the tray number plus the compartment within the tray.
I also have a bin for those parts in a high enough quantity that they don't fit the tray compartments.