This utility (swap_dll.exe) will allow you to swap the original pmmerge.dll file with the 
patched version automatically.

The syntax for adding this utility to your config.sys is:

CALL=:[PATH TO CHANGE CONTROLS]\swap_dll.exe /c[LOCATION OF YOUR CMD.EXE FILE] /s:[CHANGE CONTROLS DIRECTORY] /d:[Drive os/2 is installed on]/os2/dll /w:[TIME TO WAIT]
 
For example, add the following to the bottom of your config.sys file:

CALL=c:\chg_ctls\swap_dll.exe /cc:\os2\cmd.exe /se:\chg_ctls /dc:\os2\dll /w5
             			    (run cmd.exe)      (source dir)   (dest dir)   (time to wait in seconds)