I don't think the seating makes much difference. They are really pretty comfortable seats for a small airplane. I prefer to be near the front on any plane.
As for car rental, my strategy is to look on Travelocity or the like for a ballpark figure for the car and dates I want. Then I look on HOtwire where they will give a final total that includes the taxes and surcharges for the airport. And then I bid on Priceline, knowing what will be added on.