Just create multiple color schemes that keep the same accent colors.
In the color scheme dialog, you should leave the first two colors as black
and white. Then you can change the next two colors (Dark/Light 2, I think
they're labeled) to the dark and light backgrounds you want. Then make sure
your accent colors show up on all the dark/light colors (black, white, and
the two you create).
Then create a new color scheme with the same colors, but choose the dark
color as your slide background.
Or you can use the same color scheme and just choose the appropriate
dark/light color as your slide background. If you set the placeholder on the
slide master to use the opposite color (dark or light), it will
automatically change along with the background color when it changes.
I'm not explaining this very well today, sorry!
