I use SASHIMI.
http://www.winmo-experts.com/
If you are on 6.5 or later builds you'll need to read through the forum posts to find the fixes you need to edit in order to properly install programs to the storage card.
I personally use a combination of SKTOOLS to create CAB and reg files to depoy with SASHIMI to reconfigure my phone. I have an "auto" folder for WM6.1 and an "auto" folder for WM6.5 Depending on which OS I'm running is the one that I rename to "auto" in order to use.
I also needed to have EXE's installed directly after CAB's, or more importantly, before the REG files so that I could deploy REG entires for executables since you can't execute reg inline with EXE like you can CAB's. At least I haven't been able to get it to work.
I reprogrammed the script in order to do the above along with addind the changes for SC installations and it works great. Development is on hold because the author has an old phone. I believe he's offered it up for anybody to take over.
I attached the file I use to replace in the SASHIMI\Program\Bin folder. Make sure you make a backup of the file you overwrite.