The v0.2 of the tool, that works with ISOS, for the moment supports all ISOS except JJK-160 and 33S-2 which have different CD structures than JJK-140 and 33S-1 respectively. This will be updated soon.
Regarding what contains every CD, CD2 contains always what can't fit in CD1 following this rule:
20 --> 10
50 --> 30
60 --> 40
That means that IF target CD has no file 20, 2nd CD will have file 20 in the position of 10. However if target CD has 20 it will go in CD1.
i.e. if we want to play JOJOBA on a JOJO cartridge, the 1st CD will have correct files 10,20,30,31,40 and 41 (meaning SIMMS 1,2,3 and 4).
From the 2nd CD only interest us the files 50 and 51 which will be located in position of 30 and 31 (SIMM 3).
To make it correctly, install first CD2 (will update SIMM3) replace SIMM3 with an new one, update using CD1 and place the SIMM3 extracted in the 1st update into position SIMM5. Notice that in both updates we should keep something in SIMM5, for the BIOS to let us upgrade.
I hope it's clear now :)
Apparently there is A 2nd revision of JOJO Bizzarre adventure with date 990927. If you manage to get it please let me know.