Ebates doesn't credit any cash back on gift card usage. So if the shoes cost $100, and you used a $20 gift card, you should only get cash back on the remaing $80 balance. I learned that a few mos ago when I wanted to go completely hamm on discounts by buying discounted Nike cards, using the clearance promo code and ebates. I read the ebates fine print and found out I couldn't.
As for promo codes, as long as it's a promo code listed on the ebates FinishLine page, you should be fine. If it's not listed, it's a crapshoot.
Finally, you should be getting full credit on your WC for the total purchase, I believe (the full hypothetical $100). Oh, and it might not post on your ebates acct til it ships, though I've had to file claims in the past when I saw the purhase still hadn't showed up after a week or two. Just make sure the "shopping trip" is listed in your ebates acct profile. That way you can reference the trip # if you need to file a claim.
Good luck, and let us know how it all shakes out.