“I was going to ask, can we use the existing cc65, or do we need a special build?”
The CPU support is in ca65, and you can still use cc65 in c64 mode without problems, but if for using c65/mega65 features you'll need to expand cc65. If you want to go this way, I suggest starting with a C65 mode, that will enable running binaries from C65 BASIC. If that one works, you'll can think about expanding the compiler itself to use the new 65ce02/4502/4510 instructions.
From my experience with implementing the 4510 support in ca65, I can tell you that you should support the C65 as the primary target instead of the MEGA65.
“I've managed to get my MEGA65 to boot, though I couldn't figure out how to mount disk images, but didn't really have the time to dig in.”
As for the toolchain to use: if you're writing assembler there has been some effort on several assemblers to include the 4502/10 instruction set: 64tass, acme, ca65 are all decent assemblers supporting all instructions of the CPU, Orphis also does, but that's a pain in the a** from the users point of view.