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To find out all the skins you are using try this in the SQL Window
SELECT TOP (200) TabID, PortalID, TabName, Title, IsDeleted, SkinSrc, ContainerSrc FROM Tabs WHERE (SkinSrc IS NOT NULL)
Then check those skins for the names of the Panes, there will at least be ContentPane. Then your new skin needs to have the same named panes so the modules will be lcaoted in the correct pane.
As far as I know the panes are identified by an unique ID (TOPPANE, CONTENTPANE...), . So if the panes in the new skin have same ID, the module will alocate there.
I found this that could be useful for you maybe: http://www.dotnetnuke.com/Portals/25/CoreTeam/BlogFiles/TimoBreumelhof/DotNetNuke%205%20Skin%20Objects%20Beta%20Doc%204.pdf
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