There are a lot of things to say about SharePoint Designer, personally I like it a lot. But you have to take it for what it is and face that not all tasks are meant to be done with the tool at least not in the current version. Just the other day it hit me when I was moving things from our stagin-environment to production environment. It should be mentioned that this is a fairly small installation but nevertheless set up in an enterprise way. I had made some changes in some of the style sheets and related files and wanted to move it over to the production environment. What is not discussed that much and what is a simple but yet good function (relatively speaking) in SharePoint Designer is the Publish function. This is for some reason forgotten but I can recommend looking in to it. Below is a couple of screenshots to show you how it looks.

It should also be mentioned that this function is not for publishing whole sites lists and web parts.