Don't worry too much about losing cards to the CQ, you can always get them back later on. You actually -have- to lose certain cards to her at certain points to get other cards, too. The only thing you should take much care in is not letting bad rules spread

For omega, ake sure you spread your GFs properly between your three main characters. You don't need holy wars or any invincibility at all to beat him, just get used to his pattern so you can block his Terra Break with defend, which is an ability only two GFs provide.
When I played, I used a party with Rinoa, Squall, and Zell. Rinoa used meteor wing, Squall supported, casted meltdown, and used his limit break, and Zell did most of the damage with his duel. 'Twas a pretty easy fight for me