Is this normal Power CMS behavior?

Using: DW 5.5
Only extension are: Form Toolkit 1.0; Universal Email 4.0.1; SecurityAssist 2.0.3; CSS Form Builder 1.0.2; DataAssist 2.1.0; Design Extender 1.0.2

So I created a new site and only have these files/folders in it:
css (folder w/several css files)
images (folder w/several images)
js (folder w/several js and font files)
index.php (file)

I have two other folders with misc. images and a template folder with a .dwt I was messing with. My images folder has about 100 images that were not relevant to the index.php page im working on (only a handful are) and my css file was very heavily customized and had about a weeks worth of into it.

Using this tutorial, adding_content.html, after having watched several video tutorials:

I tried to "add content to Power CMS" by selected a small bit of content on my index.php page. I added my connection and then was asked at one point if I wanted to push the files to my testing server. I clicked OK and it started copying files.

Now here's my question and issue: Is this next part expected behavior?
Keep in mind I understand that it will create files for the CMS and the helper files that go along with it, plus whatever files are needed for the editable region/cms function. This is what happened:
It created:
admin_cms (folder)
Connections (folder)
CSSMenuWriter (folder)
install_cms (folder)
WA_CMS (folder)
WA_DataAssist (folder)
WA_Globals (folder)
WA_SecurityAssist (folder)
WA_ValidationToolkit (folder)
WADbSearch (folder)
webassist (folder)

IT ALSO AND MOST IMPORTANTLY:
Overwrote my main .css file (almost a weeks worth of customizing) with this:
#outerWrapper #contentWrapper #leftColumn1 {
display:none;
}
#outerWrapper #contentWrapper #content {
margin:30px 100px 0 100px;
}

It didn't seem to touch any other css files however I'm not sure it didn't touch or replace any js.

ALSO, it copied ALL of my existing files and folders to the testing server (overwriting my .css file with the new blank one) including all of the 100 irrelevant images, HOWEVER, it DID NOT copy any of the new files or folders it created (except for maybe some files it may have created in the images, css and js folders I already had like it did with the .css file).

I'm pretty sure this is not supposed to work this way. It did not happen in the video tutorials I watched. I have to now recreate most of my work from the last week (per usual whenever I try a new extension as they are usually full of surprises but I keep doing it - my fault)

Anyway, I guess my real question is what files and folders should I expect to see when this works correctly? I want a full list, please. And yes, I'll upgrade to 1.0.3

Thanks