File structure of published folder

Thanks for your advice.  Now I know I can publish only the changes I make.
Should I open the iWeb folder and drag only the changed pages to the server side of the FTP window? 
Can I mess up the file structure of the iWeb folder if I don't do this exactly right?

If you do a lot of updates and you want to get your web pages downloading faster, an optimizer will do all the thinking for you. These screenshots are of one of Ton Brand's Optimizers - HTML Optimizer Plus
On the first pass all the files are optimized and uploaded...
After that, Smart Handling is turned on and only the changed files are processed...
The original folder is 10.1 MB and the Optimized one is 7.7 MB. That's without optimizing the PNG images. The finished site downloads fast. It needs to since its designed to work on mobile devices.

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