Have a squint at some of Tom Whitwell's multi-board modules, eg, the new Turing Machine:
You can, although it's not obvious, cut paste between two schematics in EAGLE. So what I'd suggest is, first, work out what's going onto what board - that might be as simple as looking at layout and space, or deciding all the stuff to do with the top layer - opamps and output resistors - goes on the top, as it were - and then break the connection at those points with a named net, if that makes sense. So, for instance: all your output jacks, a + and - power jack, a ground jack, all broken out to a net ending in a label - and then another label elsewhere to indicate how those nets join.
Then you can cut one half of the circuit into its own new sch/brd pair, and connect those named points to a jumper on each schematic. Then, all you have to do is make sure the jumpers are in exactly the same place on each brd.
I'd definitely recommend going careful on support - if you've got eight pins to connect between two boards, two pairs of four will be much more stable than one big eight, obviously.
Does that help? I'm more than happy to help with layouting - it's one of the few things I'm passable at now. Is this going to be SMD or through-hole?