To determine the path to specify in your CSS/JS file link, it depends on where in the code you are linking them.
If the links are in test.aspx, then you would use the following paths:
<link rel="stylesheet" type="text/css" href="../../Theme/CSS/filename.css" />
<script type="text/javascript" src="../../Theme/Javascript/filename.js"></script>
However, if the links are in the master page, you can simply use:
<link rel="stylesheet" type="text/css" href="Theme/CSS/filename.css" />
<script type="text/javascript" src="Theme/Javascript/filename.js"></script>
This is because the master page is located in the same directory as the Theme folder and does not require navigating up the hierarchy using ../.
Alternatively, since you are using ASP.NET, you have the option to reference the path absolutely:
<link rel="stylesheet" type="text/css" href="~/Main/Theme/CSS/filename.css" />
<script type="text/javascript" src="~/Main/Theme/Javascript/filename.js"></script>
With this structure, everything is assumed to be contained within a folder named Main located at the root of the site.
UPDATE:
If you are certain that the links are correct, try running the site in Chrome and inspecting the source to determine if external files such as JS scripts and CSS files are being served and loaded properly. You may also try this in Firefox or host your site for further analysis.