If the Jaz drive co-exists with other SCSI harddrives, most BIOSes will want to boot the disk that has the lowest SCSI Id. The Jaz drive can be set to SCSI Ids 0-6, and typically come out of the box set to SCSI Id 5. Some BIOSes detect and skip removable devices like the Jaz. If your BIOS will boot from a Jaz, you can set your main SCSI harddrive to SCSI Id 1, then you can change the Jaz from SCSI Id 5 to 0 when you want to boot from the Jaz.
More typically, the Jaz drive co-exists with an IDE harddrive. Nearly every BIOS will want to boot the first IDE harddrive. Some BIOSes will allow you change a setting in the BIOS setup to boot from a SCSI device first. Others may require you to disable the IDE drives in the BIOS setup. Still others may require detaching the IDE drives physically or disabling the IDE interface.
Although running Linux from a Jaz cartridge is much slower than running from a harddrive, the Jaz drive makes an excellent ERD (Emergency Repair Disk). It's also fun to be able to just pop in some new Linux system or to try Linux on someone else's Jaz-equipped machine.
By far the easiest way to install Linux on the Jaz cartridge is simply to follow the install procedure for your favorite distribution with the Jaz drive being the only drive on the system. I've done this with RedHat 5.2, and it works perfectly. If you're not completely comfortable with doing weird, wild stuff with LILO, it's the only way to go.
If you want to do an "install" from your running system, you can often succeed in "building" a bootable system on a Jaz cartridge.
/devfiles are copied. Be sure all permissions, ownership and group ids are retained.
/jaz/etc/fstabto mount the Jaz cartridge partition(s) as appropriate. Also change
/jaz/etc/lilo.confto match as well.
rdevto make it mount the Jaz cartridge as root. Boot from the floppy when ready the first time then run LILO to make the Jaz MBR bootable.