Hello.... I need to create a very customized template. At the moment, the only way to accomplish this is by mean of modifying directly each web control (*.ascx files), the pages (*.aspx files) and the masterpage. Is this the right way to do it?
Document your changes.. I use winmerge to see if any pages change between versions and if nothing changes just overwrite with my updated documents.. if it does change its normally minor and easy to fix.
You can alter files or you can create new ones. when creating new ones I think you can upgrade more easily.
Personally I change the existing files. When I upgrade to a new nopCommerce version I would sort folder (I mostly change master/modules and CSS files by date and I can see all the files I have changed and copy them to the new project. To be sure and to check twice I would use Winmerge. very old school I know... :-)
If you gonna change your website all the time, I would use version control. Some very well know version control software is GIT and Mercurial
Also If you change/create some tables make a backup if you upgrade nopCommerce.