Saving number of kerbals in ship

If you left click on the hatch, it'll bring up a list of occupants with an EVA button next to each of their names. Then it's just a simple matter of flying them to wherever they need to be. This is the same process that you use for the stock hitchhiker pod as well.

Never did that before, but I think you should be able to do it by manually editing the saves files. More precisely the persistent.sfs file.

There is a ROSTER category located somewhere down the file where you can find all your crew members. (Lookup their name!)

You can revive them by setting their state back to 0.

(Seems to be confirmed by http://forum.kerbalspaceprogram.com/threads/41891-How-to-revive-the-%28bob-bill-and-jebediah%29)

You can as well add Jebediah to the command pod. Lookup the ship's name into the file and locate the crew = x value. Change this to the number of crew member you want to add. Jebediah should be 0.