The two designs would need to be the same number of layers (and dielectric thicknesses per layer, if you are specing that out.) Also, you'll be paying the cost of whichever board has the smallest feature sizes across both. If you are already doing N-up on a panel, the fab house might be able to combine them for you. Or else do it yourself in the cad tools, by either panelizing them yourself, or putting a good score/breakaway/board notch/etc. between the two.