Ok,
Figured this out. Maybe not the most elegant way of doing this, but I thought I would post this just in case anyone else was interested in managing their own menu. I added this at the end of my /home/tc/.xsession file:
sudo rm -r -f /home/tc/.wmx
ln -s /mnt/hda3/new_tc/flwm/.wmx /home/tc/.wmx
First line erases the .wmx created by tiny core. The second line creates a symlink in it's place to a different location. In this case /mnt/hda3/new_tc/flwm/.wmx.
So far seems to working great.