In general, a bootable ProDOS volume needs only the PRODOS and BASIC.SYSTEM
files. You can substitute a different file for BASIC.SYSTEM as long as the
substitute's name ends with .SYSTEM and has a filetype of SYS. If you have
only these two files, you boot to BASIC.
The most likely cause is that your Apple IIe is unenhanced. Only the
enhanced Apple IIe recognizes the SCSI interface card during startup. An
unenhanced Apple IIe can't start up from the device, but you can use it
after starting up from some other device.
If this is the problem, get an Apple IIe Enhancement Kit (Finished Goods
part number A2M2052, SRP).