Hi Barbara,
The checkbox in the installer will install a web-server-wide connector. If you're looking to connect different sites to different instances then you should NOT check the checkbox. Instead, you should uncheck it and install a site-specific connector manually.
Attached is a doc I wrote for Railo regarding multi-instance installs. While it's obviously old, the principals it refers to are still relevant - so with some interpolation, I believe it can help get you where you want to be with your new Lucee setup.
Hope this helps.
Kind regards,
Jordan Michaels
--
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