You should always have matching kernel and initfs or tablet may not boot. So if you flash initfs for OS2008 you should also flash kernel for OS2008.
Yes, you can flash prepared initfs image from the tablet, just run initfs_flash script with existing jffs2 initfs image.This will skip the wizard and just flash the image (original or with bootmenu, doesn't matter). There should be one or two such images in initfs_flasher directory if you installed bootmenu. If you combine this with kernel flasher you can do it in one go before rebooting to different OS200x. First flash kernel, then initfs and reboot.