Can I reuse the same JChem package on my file system to operate multiple JChem Cartridge instances?
Yes, you can. Create jchem/cartridge1, jchem/cartridge2, etc. working directories for each JCC instance by "cloning" (copying) the jchem/cartridge directory. When installing a given JCC instance, make the corresponding jchem/cartridge[12...] subdirectory your working directory (cd to it) before starting the install-interact.sh (or install-interact.bat) script (or batch file).
When upgrading such a setup, create the same subdirectory structure in the new JChem package by "cloning" (coping) the jchem/cartridge directory in the new package and make the corresponding jchem/cartridge[12...] subdirectory in the new package your working directory (cd to it) before starting the upgrade-evol.sh (or upgrade-evol.bat) script (or batch file).