Whilst players can have one install of SH3Cmdr and use shortcuts to point it to their different installs of SH3, I strongly recommend, particularly if one of your SH3 installations is NYGM, that you have multiple installs of SH3Cmdr.
This ensures, with 100% certainty, that you will not have any "accidental" cross-pollenation between your different SH3 installs. It's particularly important if one of your installs is NYGM, as NYGM modifies certain files in a way that makes their structure different from the stock, and other mods', files.
It also means that you can have unique settings and files for each SH3 installation. For example, you may want to use the combined ship skins add-on with your NYGM install, but not with your GW install. Or you may want the sabotage effects enabled with NYGM, but not with GW, and so on. Essentially, separate SH3Cmdr installs gives you maximum flexibility.
Re JSGME, simply copy JSGME.exe into each install of SH3 and run it from there. It will automatically pick up the "related" SH3 installation folder.
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