As far as her throwing a back-up ball is concerned, I would look at the results she is getting while doing so. If she does it consistently and gets decent results, I wouldn't worry about changing it. Sure, I wouldn't teach someone to throw the ball that way, but I grew up watching a lot of bowlers, particularly women, throw the back-up ball with a lot of success. If it's something she handles well, I don't know if I'd bother trying to convert her.
Additionally, be wary of coaching a spouse. My wife bowled mixed leagues with me for a few years, and it was a very tenuous situation. If I suggested she make this adjustment or that adjustment, she claimed I was confusing her. If I didn't make any suggestions, she claimed that I was just leaving her hanging out to dry and not helping her. Obviously, it was a bit frustrating for both of us. As such, if she wants to learn, I would consider having somebody else coach her. For some reason, most husbands/wives, boyfriends/girlfriends, etc. seem to take instruction better from strangers. Now, maybe you and your spouse work better together than most. I'm just telling you what I've seen and experienced. In any event, good luck to both of you!