Boats run from both.. The boat "starts" in POR and then stops at FQ and heads to DTD. They run more often at peak times then middle of the day
DTD back, they stop at FQ first then POR. If you are staying at FQ, the boat is "better" or faster then if you are in POR.
Buses also pick up FQ first and then hit main depot at POR when going to parks. On way back, they hit FQ first then POR. Again, FQ has an "advantage" if you want to call it that.
We did POR in april of this year. Loved the resorts, but did not like the buses. We are going Jan 08 and picked FQ due to smaller size and first accesss to buses.
Via boat, not a big difference, but there is one. Plus you can still use POR pool and facilities if you like.