Finally I managed to find time to configure the Motorola monitor Assist09 to the MicroKit09. It is a very small monitor that uses an ACIA (6850) and optionally a PTM (6840) to work.

Short introduction into Assist09. 

All commands and hex values should be uppercase. Commands and arguments 
are separated by one or more spaces.
A complete description and assembly listing of Assist09 is in the 
Motorola MC6809-MC6809E 8-Bit Microprocessor Programming Manual, Appendix B

Command Name  Description                              Command Entry
Breakpoint    Set,clear,display, or delete breakpoints B
Call          Call program as subroutine               C
Display       Display memory block in hex and ASCII    D
Encode        Return indexed postbyte value            E
Go            Start or resume program execution        G
Load          Load memory from tape                    L
Memory        Examine or alter memory                  M
              Memory change or examine last referenced /
              Memory change or examine                 hex/
Null          Set new character and new line padding   N
Offset        Compute branch offsets                   O
Punch         Punch memory on tape                     P
Registers     Display or alter registers               R
Stlevel       Alter stack trace level value            S
Trace         Trace number of instructions             T
              Trace one instruction                    -
Verify        Verify tape to memory load               V
Window        Set a window value                       W