Well, basically it goes like this (I don't remember now if all details are like I've done earlier, I don't have time to check or test this on real Amiga now):

1. Change partition layout type to RDB (Picture 1).

2. Click "Edit Filesystems..." (Picture 2).

3. Click "Add...". Select 68k filesystem you have copied somewhere on HD, it doesn't need to be in L: either. Filesystem will be written to destination disk's RDB block, it won't be needed to reside in any directory after it. (Picture 3)

4. Edit filesystem properties on the window which did open after you selected the filesystem file. Most important is to change filesystem to "Custom" and edit its identifier to something which isn't used on native filesystems. In this example I'm adding 68k SFS and change the identifier to SFS/05 which is in hex 0x53465305. 05 is just big enough which won't mess with usual 00 or OS4's 02 etc. (Picture 4)

5. Save changes and create a new partition. Change partition's filesystem to "Custom" and use the same identifier you used before, in this case 0x53465305. For Amiga use, remember to change max transfer to 0x1fe00 (Picture 5)

6. Save changes and maybe better replug the drive. Quick format the created partition(s).

Drive should be ready to be plugged in on Amiga. There's no need to have filesystem as visible file anywhere now on, because filesystem has been saved to the drive's RDB and it'll work anywhere you plug the drive in.