Javascript conflicts is the problem when each module uses it's own technology ( JQuery , Prototype.js , Mootools ).So there are 2 basic section that you can work with.1st) you can enable each module to be published at different menu items. 2nd) ( Code edit ) If 2 modules uses the same technologies like Mootools you can edit these modules and choose to run from one file both of them. This not means that it will work 100% because it may be using different js libraries.