Parallaxing in multiple rooms

Is it possible to have parallaxing backgrounds in a Metroidvania style map such as this?

If I place all of the backgrounds and set the background layer's scroll rates to 50, the backgrounds are highly offset and often go off screen. I tried offsetting the backgrounds in the layout editor but that didn't help. I also tried creating backgrounds individually as you enter each room, but that didn't help either.

If each room was a separate layout then this might not be a problem..but I'm using a single layout and MagiCam so.

Any ideas?

I threw a couple ideas into a cap, maybe one of them will help.

http://dl.dropbox.com/u/5426011/examples2/parallax_ex.cap

made in 0.99.96

Thank you good sir.