Im not sure whether this has been gone over before, but I would like to bring it up again, for other n00bs out there.
When I go on away missions with a SC, eg. doing a trade route. I launch the SC that I am using with a marine as the pilot. I order the SC to halt. Then I shut off power to launch control to prevent any thefts while I am away. I then eject from the craft. I use tacops to target the SC, and fly over to it and use Alt-D to enter and gain control of the SC. I go about my trade route in my shuttle confident that none of my assets will be stolen by intruders while I am gone. After I am done trading and want to get back to the CC, I fly with in 1 km and eject from the SC, using ALT-E. I fly over to the CC, land on it and enter it using /. I can then bring Launch Control back online and order the SC to RTB.
Always nice to be able to go on away missions and not worry that some intruder is grabbing everything from your CC that isnt bolted down.