First of all, jQuery is included in b2evolution, so use that rather than prototype. Otherwise there will be conflicts and errors at worst and wasted bandwidth at best.

When you're loading js libraries, use require_js: http://doc.b2evolution.net/v-2-4/evocore/_blogs---inc---_core---_template.funcs.php.html#functionrequire_js

That will only load the js if it hasn't already been loaded (provided the first plugin that tried to load it also used require_js).

Thank you.
It's exactly what I was searching for.
;)