You could use the WINEPREFIX variable and run your patch from the command line:
WINEPREFIX=$HOME/.PlayOnLinux/wineprefix/Steam wine /path/to/patch.exe
Where "Steam" is the name of the PlayOnLinux game profile ("bottle") you're trying to install the patch to (you'll have to browse to the POL wineprefix directory to find the appropriate name because they don't seem to always match what is displayed in the program) and "/path/to/patch.exe" is the full path to the patch program.
More info on WINEPREFIX if you want more details:
http://wiki.jswindle.com/index.php/Wine_Prefixes Aangepast door dedxi
