One should always set up a Project Sequence to perfectly match the source footage. Then, use the Export settings to adjust the output, as is needed. If one does not match the Sequence to the footage, there will likely be issues somewhere.
Good luck, and glad that you asked, before you had done a bunch of editing in your Project.
Thanks Hunt. I really appreciate the advice.
PS - note that when choosing the proper Preset at New Sequence (or New Project in earlier PrPro), if there is not one that matches the source footage 100%, one can choose the Desktop Project, and then manually adjust the parameters to match. The Desktop Preset allows one to customize most parameters. Also, in CS5, one can drag an Asset to the New Icon (bottom of the Project Panel) and PrPro will create a Sequence to match that footage automatically.
In PrE, there is no Desktop Preset, but dragging the Asset will work within a much more limited range, as it will try to match an existing Preset. Not as much power, or flexibility, as with PrPro CS5.