Template problem when uploading my website

The exact method of creating a page from a .DWT Template varies by version.

Which DW are you using?

In older versions it was File > New... > Page From Template
In newer versions it is File > New... > Site Templates > choose the site > choose the Template > Create

If you're using any other method than one of those two when creating a new page from a Template, it won't work correctly. For example, you can't open the .DWT Template file and use Save As to create a .html file, the links won't work.

In addition to what osgood_ has said, you may like to have a look at How to design web pages based on Dreamweaver templates

You cant be creating and saving the page made form the  template correctly as the path to your files are incorrect:

<link href="../Dreamweaver%20link/twocolumnfixed.css" rel="stylesheet" type="text/css" />

<script src="../Dreamweaver%20link/SpryAssets/SpryMenuBar.js" type="text/javascript"></script>

<link href="../Dreamweaver%20link/SpryAssets/SpryMenuBarVertical.css" rel="stylesheet" type="text/css" />

<a href="../Dreamweaver%20link/index.html"><img src="../Dreamweaver%20link/NPIS%20logo.GIF" width="100" height="68" class="fltrt" /></a>

if you look at the path to the files in a correct page such as the index.html page or cpdday.html you will see the correct path:

<link href="twocolumnfixed.css" rel="stylesheet" type="text/css" />

<script src="SpryAssets/SpryMenuBar.js" type="text/javascript"></script>

<link href="SpryAssets/SpryMenuBarVertical.css" rel="stylesheet" type="text/css" />

<a href="index.html"><img class="fltrt" src="NPIS logo.GIF" width="100" height="75" /></a>

So the question is how are you producing the new page/s.

1) You select New from template > choose the template from the site folder > then save the page into your site folder with a name.

2) Open it and start adding and editing.