Tony,

I don't use DreamWeaver, but this problem exists in GoLive as well. Get yourself stand alone FTP software like Fetch or Transmit. They are relatively cheap and are made to handle these types of things as opposed to those other multi-tasking apps.

Howdy -
Are you using Dreamweaver to update the live site? Our configuration is designed to use Dreamweaver's "synchronize" command to update the live site.
(in the Files window, there's a little box that you click to bring up a menu - choose Site - Synchronize...)

Once Synchronize is selected, Dreamweaver will connect to the remote site and compare your files with the files there and create a list. The first dialog box has a check box down at the lower left: "Delete remote files not on local drive" Checking that will delete the flak.

Next, there will be a list of files to update, delete - here's where you'll have "line-item veto" - a chance to tell Dreamweaver to ignore selected files and leave them alone.

All that said, it is good practice to have a true ftp client handy. I feel like I have a little more control that way.

hope that helps -
~beep
Yellowbeetle

So should i use a basic FTP application to do such actions such as GET and PUT and DELETE, and use Dreamweaver to do the coding and page design?

That's what we do. Never had any problem with our preferred ftp client (Fetch)