They make low rise bike shorts (short in length). Look on the TE website, or Terry makes some also. I would definitely do the bike short thing (and ditch the thong- really- your girly bits will thank you). Even tho you're only on your bike an hour a day, that's like 6 hours in girly-bit time.
If you have a store near you, go try some on. If you don't want a very big chamois, then buy some triathlon shorts (they come in very short lengths, and the chamois is very thin- thin enough for padding support, but not big and bulky like cycling shorts designed for longer rides).