AFAIK the Windows and Linux versions of BOINC run at boot time, but for OS X you have to run a simple terminal command to make BOINC run even when no one is logged in.
But each time you reinstall or upgrade Manager you have to remove it from each user's Login Items if you don't want or need Manager to be running in addition to BOINC.
This link will walk you through how to run make BOINC as a daemon, or service, and it shows how to make a simple text file that prevents Manager from being added to each user's Login Items. You can even edit the file to make Manager run at login for some users and not others.
Tools for Mac OS X
OMG I finally got my second star, I am regular lol!
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