One more question on this. The original render that I did out of AE does not have the "field render" setting turned on, will that cause an issue when I run the encoder preset, or will the "upper fields" setting in the preset handle it fine?
It will make a very big difference if your source video is interlaced. You'll have to check that. If it is interlaced, then I recommend re-rendering, setting the correct field order in the Render Queue's Render settings.
Just so you know, It's easy to create your own sets of Render Settings & Output Modules. It's just as easy to change the defaults for them. If you know you're making a half-dozen files with interlacing in the ProRes 422 codec, for example, just make new templates and select them as the defaults.
KGAN (CBS) & KFXA (Fox) Cedar Rapids, IA