I think the most important factor about a FF program is how well it fits your flying patterns. Being based out of Houston, Continental seems like the best fit. I would have her concentrate on Continental for work {including credit card}. On the side you can have her do AA on a personal basis.

Concentration works best. Also remember that Continental and United will merge so you might decide to use United as the secondary since the FF accounts will eventually merge giving you a larger mileage total.