Depends on what you think you'll use your logbook for. Most airlines and similar have a correction factor to account for this. FedEx, for example, adds .2 to each military sortie. So in that case, you'd be better off having the .mil time logged our way. If you won't be applying for a place that uses a correction factor, you might be better off logging the civilian way. I log military flights the military way and civilian flights the civilian way, then I'll add the correction factor if I can or need to. The difference likely won't make or break your application.