Do I use them through common application or do I print them and send them to the colleges? I’m really confused.
They’re separate. The fee waivers from college board can be used for colleges NOT on the commonapp, such as (probably) your state flagship and other public colleges.
Your guidance counselor can also fill this out in addition:
http://www.nacacnet.org/studentinfo/feewaiver/documents/applicationfeewaiver.pdf
For the CommonApp, you click “fee waiver” in each case AND your guidance counselor must click " Fee waiver: eligible for fee waiver from college board" on that form. And then you’re good to go. 