They'll do a level match, BUT you'll only earn points for the line you cruise with. For example, I have a cruise on Celebrity coming up in October. It's worth 30 points. While my status will be reflected when I cruise Royal again next year, those points I earn in October will only count towards moving up in Captain's Club, not Crown And Anchor.
Conversely, my cruise after that is in June on Royal. That cruise is worth 15 points, which will count only towards my Crown And Anchor points, not my Celebrity points. That said my status will still be reflected in Captain's Club.