Chris,

I do not know the answer to that one because I don't go about it that way. I just modify the ascx files and do not use the parsing method. Though I would imagine that it would parse the container files in the same way that it does the skin file.

Maybe try this... in your Dark Knight standard install go into the containers folder and copy a container folder. Rename it to whatever you want, then start modifying it to test around. Once you get it styled the way you want it then just copy that container folder into your site and you should be able to access it.

If you're seeing a new skin on the site then you either changed it in the Page Settings of that specific page or in the Admin > Site Settings > Appearance section. You can have a skin be applied site-wide (in the Admin settings) or be designated at the page level (in Page settings). 

One thing I should add is that if you do not specify a pane called "ContentPane" then the skin may error out and then revert back to the default / fallback skin.  Skins must have at least one pane named ContentPane. If you don't have that pane in your skin file then add it back and see if that fixes it

<div id="ContentPane" runat="server"></div>