The Unidisk 3.5 should work with any 800k formatted ProDOS disk. For best performance they should be formatted for 4:1 interleave. By default, Macs likely format them at 2:1 or 1:1 interleave. Formatting them in a Unidisk should give the desired 4:1, and ProDOS should install boot blocks.

The SE should have PC Exchange or the older "ProDOS File System" extensions installed (comes with the Apple IIe card) to natively mount ProDOS disks.