It's not correct to place the template files directly into the directories specified in the options. You will have to move your template files into subdirectories of the template directories.

Assume, you have a file 'Love Letter.tex' you would like to use as a template for new documents. To do so, create a subdirectory called 'Letters' in one of the directories specified as template directories in the options and move your 'Love Letter.tex' there.

Now choose one of the commands from the 'File' menu, that will open a template dialog and you will see, that the dialog has got an additional tab called 'Letters'. This is the tab for the subdirectory, you have created and on this tab you will find all files, that found in the directory, including your 'Love Letter.tex'.

Please read the online help shipped with TeXnicCenter for additional information on how to use templates.