If your flashing a rom, read this thread
Re: Templates: Custom Start Menu's for your ROM - 9/29/08
Post #5 is my updated method and will work with most SYS bases. Use the provxml to delete shortcuts, and the initflashfiles.txt to add them back in where you want them...I haven't made an OEM for the touch pro yet, but I'm sure it's the same minus a couple extra programs...