I have always been uploading my websites with all source code and everything. Maintaining the website this way has been easy, when updating a single webpage I just need to reupload the .aspx and .vb files for that page and I'm done, easy.

Now I am trying to learn how to use precompiled websites using the "Build" > "Publish Web Site" features from the visual studio menu.

Here's a few this that I need some advise on:

When using this feature visual studio wants to delete everything from the destination and then publish. The problem is the website allows users to upload files to the website and this will delete their data. Is there and easier way to do this?

This may be the answer to the above question, lets say I publish to a folder on my desktop instead and only upload the files needed. I noticed that If I change one webpage I have to reupload all webpages and files from the bin folder. Is this how it is meant to work?