The Emulator and the ROM have been adapted for the new board. You can check out branches x16_board_r2 in the source of the two projects. The official reference manual has also been updated.
In short, these are the major breaking changes:
RAM and ROM banking is done through magic zero page locations 0 and 1. Up to 512 KB of ROM are now supported.
VIA#1 is now at $9F00, VIA#2 at $9F10
YM is at $9F40
All I/O (PS/2, Controllers, Serial) has been moved to VIA#1 PA and PB.