Mud Eagle,
The biggest hassle comes for the multi-place guys when they have to start figuring out FAR PIC and SIC time using AF "primary" and "secondary" time, respectively, for different airlines' applications; you really can't because they are not necessarily the same thing. It's a real headache to go back and figure it out if you haven't kept track of it as you flew it. Without other information, it is like comparing apples and oranges.
The "ground" time thing, though, is really not that big a deal since the mil/civ difference is only about .1 or .2 per sortie. Many airlines let you convert a portion of your military time anyway because they don't want you to lose that time either. If they don't let YOU do the conversion, they do it themselves in various ways, depending on the airline. They may not actually convert hours or sorties, but they take into account that the military tracks time differently. Some even weight the quality of time differently ( IP, fighter, etc).
I would NOT go back and change anything in my logbook, but that's because I'm lazy and I like a neat logbook. I wouldn't keep separate logbooks either. Instead, you can, quite properly, start logging your civ AND mil flight time IAW FAR Part 1.1 definition of "flight time"; "Pilot time that commences when the aircraft moves under its own power for the purpose of flight...". Just don't convert THAT time when an airline application allows you to convert your military time.
Strictly speaking, if you are going to keep a logbook for FAA purposes, it should be kept in accordance with FAR Part 1.1 and 61.51 and then you just don't have to worry about it.
I hope I haven't muddied the waters even more.
Fly Safe!