Hi, ive had the same problem as you. I was trying to add the floating div pane to a minimal master page. But it didn't work.
Thats because you need to have the div that tells sharepoint where to place the ToolPane, without it sharepoint will just place it where it wants to.
Here is the div that will hold the ToolPane on your page:
<!-- This Div tells sharepoint where to place the ToolPane -->
<div id="MSO_ContentDiv" runat="server">
<!-- /ToolPane div -->
But now that i got the ToolPane floating, none of the Ok/Cancel/Apply buttons work.
Let me now if they work for you.