should be able to put that e-cert into your "my wallet" account. customer care may have to assist with that if it was issued 30+ days ago (i'm foggy on the rules). once you've put the funds in your my wallet acct, just apply the companion fare code, book your flights, and use my wallet funds when entering payment info.

i don't believe there's a way to use multiple discount codes on AS.com, but you can use an upgrade cert on a companion fare'd itinerary after ticketing.