Here an image of the MicroKit09 with the ACIA/PTM extension for usage with the Assist09 monitor.

The I/O board and the MC6821 is not used in this setup. 

Just tried to set a breakpoint to test the PTM, and it worked!

>D 1000

>D 1000

      0  1  2  3  4  5  6  7  8  9  A  B  C  D  E  F
1000 12 12 12 12 12 BE 10 67 A9 FF FF EF 00 DA 10 24  .......g.......$
>B 1002
1002
>G 1000
PC-1002 A-00 B-00 X-20FE Y-F002 U-18C2 S-1851 CC-D4 DP-00
>

The Assist09 monitor is described in the Motorola MC6809-MC6809E 8-Bit Microprocessor Programming Manual (M6809PM/AD, 1981), Appendix B.