On the MESS entry for Apple II, it gets a bit complicated. For a single disk with .do, .dsk, or .po extension (open the zip file to check) you could use "apple2e -flop1" (add other parameters before the "-flop1") and if the file has a .nib extension check "Use Custom Command-Line ..." and type in "apple2c4 -flop1".
If there are two (or more) disks you need to check "Use Custom Command-Line ..." and type in "apple2e -flop2 "<full_path_to_second_disk>" -flop1" (no need to add the first disk as LB will automagically add it). You may have to experiment with which disk to use as a second disk. Some games need a blank disk to hold your info, scores, saved games, etc. and some have several scenario disks so you need to make several LB entries, one for each scenario.
Also, there should be an entry for "Apple IIGS" also. That would be "apple2gs -flop3" for .2mg Apple IIGS disks and, checking "Use Custom ...", type in "apple2gs -flop1" for Apple II disks. See above for how to add more disk images. Hope this helps.