Call old me dumb, but I cannot quite follow your post. Perhaps you would not mind describing the problem(s) you are experiencing again, in more detail, so others can try and help you.
What format do your templates come in? HTML?
What error message do you get when the uploaded web pages fail to display in your web browser?
"When I open up the FTP program again I am able to view it" - do you mean when the FTP program is running, you can see a listing of web pages/files, or do you mean when the FTP program is running, your web pages suddenly all load properly in the web browser (and the web pages will not load in the browser when the FTP program is closed)?