There is no onload conflict with Facebox, it uses the jQuery document.ready method, which in turn uses the addEvent/attachEvent methods, which don't conflict. Multiple stylesheets will only be a problem if the actual styles in them contradict each other. I'm guessing that you are using another library with the other script that conflicts with jQuery. jQuery can be run in no conflict mode though that doesn't always resolve all issues with other libraries. Often the best solution is to find a substitute for the other script, one that functions like it, but that uses the jQuery library.
If you want more help:
Please post a link to the page on your site that contains the problematic code so we can check it out.
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