as for the order, never mind. It's simply in alphabetical order, so it's normal that it appears 1080p, then 480p, and finally 720p

Oh you just mean the sorting of the profile list?  There's a trick for that as well - put a space in front of the 480p and 720p profile names and they'll be listed first (it also visually aligns the text with 1080p as well).

The opposite is to put a ~ character at the beginning of the profile name which will move it to the end of the list.

That's what "Source frame area" is for - it refers to the actual resolution of the source video stream.

In your case, you should be able to get the correct condition by simply adding a "minimum" to each profile like you stated, like having the 1080p profile only apply to videos with a height larger than 932.

If this doesn't work, the then trick is to simply make redundant conditions, like specifying a minimum and maximum for framerate, source video size, and video frame.

What if 1080p, 720p and 480p aren't in the right order? Is there a way to re-organize them, or is the only way to delete and re-create them in the right order, or set conditions that ensure only one profile will match (such as Height > 600 && Height < 1000)

Also, it is insisting on taking the "720p 30fps" profile for a 1080p video... when the "1080p 30fps" profile should be selected. I'm opening the raw video through an AviSynth script, I don't know if it messes things up.