hiya Jackall,
Any changes that you make with a VSD website, need to be done within the program itself. If you edit anything outside of the program it will be lost if you update with VSD again as VSD does not have any import capabilities to import your changes so it will not know you did any and will just overwrite them.
What lots of people do is use VSD to get their site to a specific point, usually where the layout is what they want it to be, colors styles etc. and many times all the main content of the site etc. Then they take the HTML Editor and do the editing in there from that point. That is of course, if you have decent knowledge of HTML and CSS to do that with. Since VSD writes in a very different style of code from normal HTML it can be tricky sometimes, but once you get the hang of it, it's not too bad.
Just keep in mind you cannot go back to VSD without having to incorporate your changes manually within VSD again to have it be the same as what you edited in the HTML Editor. VSD uses the .vnu file which isn't editable manually, so all files and folders and anything in your site is inside that .vnu file. Nothing outside of that file is recognized.
Hope that all made sense and good luck whichever way you decide to venture your editing