I have two ways. I keep a Borka torque kit in my war bag and I keep a few index cards with all my different offsets written down. The second way of keeping zeroes managed is with a Kestrel. I keep each barrel listed as a separate rifle, and if I use a different bullet/load, I keep that listed as a separate rifle (my 25 Creedmoor, 6.5 Creedmoor, and 25 PRC barrels each have at least 3 different combinations, so each combo goes in under its own name) and then I can set the offset under zero height and whatever the Kestrel zero windage offset is called. I prefer to zero my scope to whichever load impacts lowest on the target, so then all my zero height offsets are positive, meaning I just had to add whatever extra clicks I needed in elevation, but that isn't as important as it used to be now that Kestrel allows negative height offsets
Edit for a typo