My questions is what should I shoot it in? 60fps or 25fps? NTSC or PAL?.
That's way too broad a question for a forum about NLE software. The simple answer is, "whatever you want." The less-simple answer is, "it depends." Whether you shoot 60fps or 30fps or 25fps or 24fps or XXfps is all about the look you want, so experiment. NTSC and PAL don't have any application to HD video (despite their regular use to label certain HD formats as such).
What really confuses me is the loss of quality from the camera to online. I find that sometimes I have to import the footage (from other video cameras I have had – Sony and Canon MiniDV’s, Panasonic HS300, GoPro Hero etc) into Premiere, edit the clips, export to a file, then import into AE and add effects, then export once more. Each time I try different formats and each time the quality differs but I seem to lose plenty of quality along the way. I know it’s not simple but for this music clip I would like to learn a bit more beforehand, what the correct workflow would be to minimise loss of quality, so I am better prepared.
With relatively few exceptions, you don't have to worry about this--you certainly don't have to worry about this with 7D footage and Premiere Pro and After Effects. Both programs support the footage natively; it's more a matter of learning how to use the suite applications in a manner that avoids exporting to intermediate files. Dynamic Link is one way, but you can also import a Premiere Pro project/sequence directly into AE. A high-resolution intermediate is another way. There is a whole section of the help documents that describe the interoperability between the applications; reviewing it closely will help get you up to speed, so that you can ask more specific questions about workflow, etc.