CompactPCI x86 single board computers (at least those we make) are just your ordinary PC, with lots of features crammed onto the main board. The backplane is a PCI expansion bus; so if you want to plug two SBCs, one of them will have to be capable to run as a peripheral board, not a system CPU. This will not be a dual-CPU system then, but two systems running in one chassis - one "owning" the expansion backplane, the other being isolated from it.
If you're buying those used, take care that you get the "rear I/O module" boards as well. This is where most of the usual I/O ports are, and if you don't have it, you won't get far.
CompactPCI slots are electrically PCI, but they're mechanically quite different.
PICMG are computer-in-a-slot that takes you straight to standard PCI and ISA slots, desktop form factor. It's just a modular approach to building a non-rugged computer. Here, you get to use your ordinary PCI cards.