Just wondering if anyone can answer this for me:

I have shot all my footage in a canon hf100 in pf30 mode. As I understand it, despite the name of the mode, all footage is always wrapped in a 60i "container/stream" (not sure which is the best term).

So, would I be advised to deinterlace the footage to true 30p? Is the "deinterlace" checkbox intelligent enough to output to 30p (as opposed to trying to make a 60p file)?

Deinterlace will convert 60i to 30p, however that is not needed for pf30 sources. 30p in 60i is still 30p, without deinterlacing. Under Neo Scene or HDlink just convert with deinterlacing or pulldown removal.

I'm no editor, but there is no need to de-interlace 30F footage, it's proper progressive as soon as you ingest it to the edit suite. This is how HDCam works too, it's PsF (progressive segmented frames) meaning it's stored as 2 fields instead of 1 frame, but it's basically the same.
Someone correct if I'm wrong!
Steve

So can I create a 1080p sequence in PPro and edit the pf30 (1080i files) footage in it?

I'm thinking that if I make footage in AE and want to put it on the same timeline as the pf30 camera footage, then I wouldn't have the option in AE to make pf30 60i videos would I. And making real 60i videos in AE would be bad because I'd be introducing interlacing to the project.

So it'd be best to either deinterlace the pf30 footage in remaster when i convert so that I have true progressive footage, or else just make a 1080p sequence and drop the pf30 footage into it.

Just drop pf30 footage into a 30p project. In AE you many also need to interpret footage as progressive, but no deinterlace is required, nor is it good for image quality.