Hello Ian Johnson,
My approach is almost the same as yours.
1. Create two folders with the names of your skins under one of the themes you use. - let's say Skin1 and Skin2
2. Then in your skin file put the line below
|<%@ Register TagPrefix="telerik" Assembly="Telerik.Web.UI" Namespace="Telerik.Web.UI" %>
|<telerik:RadTabStrip EnableEmbeddedSkins="false" runat="server" Skin="Skin1">
By doing so, Skin1 will be set as default and embedded skins are disabled.
3. Then drag and drip two controls on your page. One on the header and another on the footer.
4. In edit mode of the control change the Skin property with the names of your custom Skin.
the Telerik team