AE can take both interlaced and progressive at the same time. It’s composition settings do not even have a “take only fields settings.” The only place where fields are, are in interpret footage command in bin and final rendering output. You may ask, what happens if I mix interlaced and non-interlaced? Well, if you have interlaced and encode to fields [OFF] then, you get a crappy deinterlaced video because AE has a bad built in deinterlacer. If you had to export fields [OFF] then get Algolith for AE because it is the only thing close to 100% original for removing scanlines. The other export option is fields [on]. Your interlaced footage wouldn’t lose any quality, but what about your progressive footage?
Well AE does have a built in re-interlacer. It simply puts each field half the time a frame is shown. There’s other field re-interlacers such as fieldskit re-interlacer that supports more options such as:
Half Frame Rate 59.95p to 29.94i
Keep Frame Rate destination 1/2 duration
Field Blending mix fields but you can’t undo it later on.
Hope this helps. Keep us apprised and good luck on your project.