I am partaking in an independent study, and there is a proposal form that I completed detailing what the independent study is about. It has official signatures from administrators, etc. On many of my portals, it indicates that the best way to submit supplementary materials is through that portal. Should I have my counselor fax the proposal form to them to make it look more official or submit it myself through the portal?
When all else fails, follow the instructions. 
Submission of supplementary materials is your responsibility, not the GC’s. You GC (or teacher) can speak to your independent study on the recs. Whether your proposal warrants being submitted as a supplement is another question entirely.