Safety pilot - you can log this as either PIC (if you are the PIC as defined by FAR part 1) or as SIC (if the pilot flying under the hood is the PIC as defined by FAR part 1).
If the plane requires a SIC, then whoever is PIC logs PIC and whoever is SIC logs SIC, unless the SIC is flying and is logging PIC under FAR part 61 sole manipulator clause. Then both log PIC..
A safety pilot becomes a required crewmember if the the pilot flying is under a hood. That is why it becomes legal to log SIC even in a single engine GA aircraft.
Total time - there is nothing that says total time has to have a corresponding PIC, SIC, Dual Received or Dual Given entry. Total Time is not even defined by the FARs. Many airlines use TT = PIC + SIC + Dual Received as a quick check of TT. They don't expect it to be exactly equal, but if it is not close, they might question / check your logbooks more.
As far as combining military and civilian time in a single logbook, I recommend it. But to do so you need to keep track of the block out and block in times for your military flight. This way, there is no need to wonder if you should apply a conversion factor or not (some airlines allow it and some don't. Further, they may have different factors. This way you know the exact civilian hours.
Remember there is a remarks section,. Use it to explain why there is a TT entry without a PIC, SIC or Dual Received entry. Annotate it's a military flight with the block out/block in times. Etc.
IT's your logbook. Except for a few entries required by the FAA you can maintain it and log flights however you want.