CSS in Cpanel

Hello,

I am a new user to cpanel. I have created websites before for fun and friends but now im working on something for my church. Cutting to the chase I created my html site pages from a template in dreamweaver. I did this so when I had to update I could do it across the board. Loaded my files into the public area of file manager, uploaded images into my images folder. When I go to view the page the margins are not as I designed and the css style sheet from the template does not apply. Do I need to create a new root file or something to place the css .dwt file into so it will apply to the pages I uploaded. thank you for the help because this is really wracking my brain.