Best workflow for interlaced footage?

I’ve been working back and forth between Monet and Mocha. The snag I run into is when to de-interlace. The process I’m using is exporting the tracked corner pin data into After Effects which gets applied to a pre-comp containing the new footage. The source (tracked) footage in AE is upper-field first, and is therefore interpreted as upper-field first. In the end the comps will be rendered back out as upper-field first Quicktimes (Avid DNXHD).So after all that here’s my question. When in Monet or Mocha, do I need to interpret as interlaced or is progressive fine considering that I’m exporting the tracking data to AE and then applying that data to a layer inside a comp containing an interlaced clip? Do I lose tracking information that won’t be apparent until I watch back the final rendered clip on an broadcast monitor that displays fields? The problem is that de-interlaced footage plays back terribly in Monet/Mocha. I find it almost impossible to tell if I have a good track or
not because of the constant back and forth movement with the fields so I usually just interpret the clip as progressive. Any suggestions?

Sean