To make this type of thumb drive persistent:
First divide the thumb drive into a FAT32 partition and an ext2, 3 or 4) partition. Label the ext partition casper-rw.
Install grub to the FAT32 partition and save your iso files there also.
Then edit the menuentry line in grub.cfg as shown below:
linux (loop)/casper/vmlinuz boot=casper iso-scan/filename=$isofile quiet splash noprompt -- persistent
If you want a separate persistent Home make another ext partition and label it home-rw.
Some people believe using ext2 for the persistent partitions will make the flash drive last longer, I don't believe it is an issue.