There shouldn’t be a big problem when importing, you just have to make sure that your file is interpreted correctly by AE with lower field first and the right pixel aspect ratio
Try using multiple mattes with masks. If you can seperate the different shades of green and use the matte choker you might be able to get a good key without reshooting. Worse case scenario you could always roto it out =P
You probably would want to go and get C4D. It has the easiest interface to work with, and intergrates very nicely with AE. I use 3DS Max, because of some features it has that C4D doesnt, but for a beginner C4D would be the way to go.