I also wanted to know how people handle situations where the same drill bits are used for multiple kits. I learned the hard way to have a set of bits reserved exclusively for pens and turning, even if it means duplicating general use bits. I don't abuse them by drilling things I shouldn't, and more importantly I can always find them when I want to make a pen.
Ahhh ... ORGANIZATION ... the problem that we all face, sooner or later and usually sooner. Yes, keep your drills exclusively for pens ... that's one thing.
I use a compartmentalized clear plastic box (with lid) for bushings ... compartments labelled ... bushings in that compartment held together with a tie wrap and a tag specifying what pen kit they are for. And, of course, you have to be meticulous about putting things back and in the right place after using.
I also keep my new kits in clear plastic boxes ... labelled by kit name ... one box for each kit type (unless you have only a very few kits on hand).
I have about 2 dozen different sets of drill bits - some for metal, some for wood, a few carbide tipped, cobalt, TiN, some for concrete, some cheap, some expensive all located in a cabinet under the drill press. I have two of the 115 piece sets of Letters, Numbers and Fractions, one in cobalt. I Zalsohave several sets of metric. The 115 piece sets do well as substitutes for normal pen sizes on occasion. And then there are my pen bits, kept separate. I have a rack I made some time ago in which I keep them.
Keeping bits and bushings together - that is too much organization for me. Kits - in the Dollar General $1 semi-clear shoe boxes.
All of my kits are kept in plastic shoe boxes in zip lock bags sorted by pen design. The zip lock bags are identified by metal type. Makes inventorying a breeze for reorders. All my bushings are kept in bobbin boxes (Art-bin) I get from Joann's. I take the label off the plastic bushing bag and tape it over the compartment that houses the bushing set. Never had a problem with it. I keep all the plastic bobbin boxes in a drawer on the turning bench with a very small foot print. I buy American made drill bits from a specialty store in Great Falls. Not sure of the name but I have the part numbers that you can probably look up. All my drill bits are stored, again, in plastic boxes sorted by size. All my drill bits are HSS and although they aren't really expensive, they're not cheap. A 7mm bit will cost around $5.90 each. Bought cheap ones in the past and had nothing but trouble with them. the other thing I do is keep all the original boxes from items like chucks, mandrels etc. Easier to store and I.D. later. Hope this helps a bit.
Pictures are about 3 years old but hopefully you get the ideal. Also sorry they are burred. I keep the bushings in the small bins and the kits in the large ones all labeled with a label maker. I keep the " plastics" in a separate container, wooden blanks in my lathe bench with drills bits above them.
I was going to use prescription bottles for my bushings, as I am getting to the point where I take enough meds to keep up the supply. Then my insurance company switched to 90 supplies and that was that. Now I use plastic boxes that were originally designed for storing beads. My wife still hasn't figured out why she doesn't have the boxes she thought she was going to use...
I use clear the type of plastic boxes that are designed for storing skeins of thread for counted cross stitching. It has compartments which I use to store the brass tubes and other parts from pen kits, and the corresponding bushings, and a larger compartment that is long enough for a drill bit and/or the ink reservoir/cartridge/refill. The boxes are short, stack-able, can be labelled on the end, and are very affordable. A local craft store where I live sells them for a dollar apiece. So I have everything for each type of pen or project together in one box.
Bushings- 16 drawer parts cabinet with drawers, mounted to the wall. I keep them in their bags. Drill bits are kept in their cases and stored in a pencil box from $ Tree. Pen mills are kept in their factory case; got the starter set from Woodcraft.