If you are talking about breaking "user" scripts from your view and putting them in a separate folder for testing your javascript, then yes, you can put them in a folder of your choice.
However, I would not recommend placing them next to your view ..., which will create a dirty project structure and make it much harder if you ever want to minimize your javascript.
I generally leave the framework files in the framework in the Scripts folder for the reasons that Mystery Man mentioned in my answer, however I put the "user" or related javascript files within /Content/js/
.
To link to them, you simply added a link to your view or main page (layout):
<script type="text/javascript" src="@Url.Content("~/Content/js/somelink.js")"></script>
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