You could keep them together in those battery carrier/protector/ case things - These.
Simple but effective, rubber bands round them.
Paper labels on each of the pair.
I like to label my eneloops on the white top of the cell with a fine permanent marker. The positive button keeps it from getting worn off very quickly.
Other options include more shrinkwrap and attached labels, but i tend to just write a a few times on each cell with marker and refresh it as needed. Redundancy helps since it won’t all get worn off at the same time
I have taken to writing where I bought it and the date, numbering 1, 2, 3 etc or 1,2 if paired up then covering that with 2” wide clear packing tape. The packing tape is strong, won’t peel off easily and is thin enough to not hamper the cells going into the battery tube.
I tried clear shrink wrap and in many cases that additional layer made the cell to big to fit in the light. I am also going to start putting a very clear solid + in Red at the top in 4 places around the diameter before taping to aid in placing the cell in the charger. For some reason panasonic has labeled their cells in such a way that they appear to be backwards, doesn’t seem intuitive. And Samsung 20R’s are not quick to identify positive pole at a glance. I need help with a positive identifier to ensure I don’t mess up. Get in a hurry sometimes, although I’ve been good about not hurrying so far where the cells are concerned, only inverted one in the charger once. But what can it hurt to have a nice solid red + identifying the positive end?
I use a label maker too. It provides legible text, plenty of characters which is important with all the cells I have, and comes off cleanly. The only problem is it comes off too easily, especially the top clear layer. I have to remember to press down the label again occasionally.
Additional battery info goes into a spreadsheet. I'll need that spreadsheet soon to match sets of cells.