Sorry ... I decided to postpone my comment to the answer.
I personally add all my JS to the ScriptManager. This helps reduce the number of Http calls the page should make.
ScriptManager1.CompositeScript.Scripts.Add(New ScriptReference("~/Page/To/Jquery.js"))
But this is only if you are already using ScriptManager on your page
In addition, if you do not want to add it from CodeBehind, you can do it directly on your page.
<ScriptManager> <CompositeScript> <Scripts> <-- your scripts in here --> </Scripts> </CompositeScript> </ScriptManager>
So, having done this, you will be able to add all your JS in one HTTP request, and not have several different requests at once.
Then, in the ScriptManager tag, you can add LoadScriptsBeforeUI="false" so that they are placed at the bottom of the page.
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