everything depends on where you want to place the jQuery module. If you want to place it on your custom module, page, etc. the it is up to you where to place it (wherever best suits you). If you want to put a jQuery module inside the MonoX Core functionality then the best place to put the registration of jQuery module would be a Master page (your custom master page visually inherited from MonoX.master) or base page (also your custom base page inherited from MonoX base page).
To help you more you will need to explain where exactly you plan to implement jQuery module ?