I have no idea about the pros and cons of using persistent changes vs. using a seperate partition to save changes. However to make bt boot into a desired method, edit your /boot/syslinux/syslinux.cfg file on your fat32 partition. Move the section of the LABEL that you want to boot to the top. This section usually includes a LABEL, MENU, KERNEL, and APPEND line. Then set TIMEOUT to 1, and restart.