Ok, here's the solution I found while using Battle CD 48 Side B. There was no hax (paralysis, freeze, critical hit, etc):
1) Lugia uses Icy Wind, so Have Latios used Protect and Latias use Thunderbolt against Ho-Oh
2) Have Latios use Psychic on Ho-Oh, and Latias use Thunderbolt on Ho-Oh.
3) Finish Ho-Oh off with Latios and have Latias use Recover.
4) Have Latios use Memento on Lugia, and have Latias use Recover.
5) Use Thunderbolt on Lugia.
6) Have Latias use Recover when it will be KOd on the next turn.
7) Repeat until Lugia raints from Thunderbolt.
Keep in mind that Lugia and Ho-Oh sometimes switch targets, in which case they mostly attacked my Latios when I used Protect. Still this is a decent way to be the Battle CD. Try and tell me how it goes.