This just in, Deepstar has made it to Mars in real time. The ship left Earth at 2:23 AM 7/7/2009 in real time or Fri Jun 19, 11:43 2020 in sim time. And made it to Mars today at 6:08 PM 2/4/2010 or Dec 31 3:01 2020.
It was a long journey and I spent the 7 months building a lunar space station as stuff like that.
I've been planning something like this for a long time but haven't gotten down to it yet; my target is Mercury because it's closer, being a 3-4 month trip rather than 6-7 months.
I would do it like this: shut the computer down at the end of the day like I always do, and even close orbiter when I am not using it. When I want to check up on my ship (will be a Shuttle-A named "ALICE"), I go into Orbiter, bring up the scenario editor, click "Date" and then click "Now" to update. I can always conduct plenty of LEO missions in a DG-IV while ALICE makes her way to Mercury, and even run a few lunar hops in a separate Shuttle-A known as BETTY.
My biggest fear is being at school or in bed or something when a major course correction comes due.