Though it is easy (as I wrote above) to make separate ground planes even automatically, I use another approach. Even with two-sides board, if good traced, it is possible to make a most part of the bottom layer a large ground plane. Especially, if the most passive components are SMD. But such a design requires
to work very accurate and redesign the ground planes many time to get as much
connections of the ground between other wires, as possible.
You can see such a plane in attachment.
With such technique I have nice working analog/digital boards with more than 12 bit resolution.
Sure, such work cannot be done blindly. Better if the same person designs both schematics and PCB.
Varuzhan