There is a setting for what field order to export in in adome media encoder. You do have to make sure premiere knows what field order the source material is in though, the commonly used lossless video formats (
huffyuv, lagarith, utvideo) don't have any way of letting an application know. If you are dealing with DV or mpeg2-encoded material, premiere should recognize it automatcially as long as the files are encoded correctly.
You do not want to save interlaced material as progressive in a lossy format like mpeg2, that will certainly create artifacts.