Making a theme NeoDock compatible is easy. If you have read "How to make NeoDock Manager see my Plugins?", then you might have already figured it out. The Neo Dockstation is nothing but a layout switcher, using some markers on the theme XML file to figure out what to replace for what. So, you just need to set those markers on your theme layout file.
Any theme file for the Neo interface has two plugin entries - one for the top status bar and the other for the Neo plugin. The markers are placed for the top status bar plugin - the first <plugin... entry in the XML file.
1) Place the following line before the start of the plugin tag.
<!-- NeoDock Markup START - DONOT CHANGE THIS LINE!! -->
2) Place the following line after the end of the plugin tag, i.e. after </plugin>
<!-- NeoDock Markup END - DONOT CHANGE THIS LINE!! -->
Since these lines are marker, you must place them in separate lines, with no spaces or tabs before or after them.
With that, the switcher can now work with your theme. Do take a look at the NeoDock.home.xml file in \Application Data\Home for a complete example.