Tim-
Is this for a custom skin for your own use or are you creating a generic skin control to package for others to use (across different skins)?

One option:
If your skin control "surrounds" the content area (as you described) you might do better to re-define the visual portions of your skin control as empty container elements in your skin (not in the skin control) and have your skin control dynamically fill those containers by ID reference.  Your skin control will not itself have any graphic elements to it -- it simply assigns appropriate CSS/content to existing page elements (the empty elements).
 
To put it another way:  think of the empty container elements as your skin-within-a-skin and your skin control as your specialized content manager.  Together, the two make something similar to a mini version of a site skin and DNN.  Note that this approach tightly integrates your skin control with its host skin so it's not a good generic solution if you intend to leverage the control across many skins.
 
-mamlin

Hi,

Brief explanation of a hack we use:

- DNN looks at server controls directly under the skin control to find available panes
- Those controls must be of one of these types: td, div, span, p
- DNN will not look for panes in nested server controls, such as controls inside a skin object

However... (this works in DNN 4.9, not tested in DNN 5):

- You can dynamically register Panes with the ActiveTab.Panes collection to add panes that are defined in nested server controls
- The pane control must be of a supported type (td, div, span, p) with the runat="server" attribute
- When you register the dynamic pane, you must use the UniqueID of the dynamic pane control, relative to the skin object:

string relativeUniqueId = MyNestedPaneControl.UniqueID.Substring(MySkin.UniqueID.Length + 1);
PortalSettings.ActiveTab.Panes.Add(relativeUniqueId);

- You will then be able to add modules to this pane using standard functions, such as the 'add module' from the control panel

Limitations:

- the pane name will look somewhat ugly in the panes dropdown list at the top (the pane name will be the relative unique ID, such as MyContainer$MyPane)
- layout mode will not show this dynamic pane (but view and edit will work fine)
- this may break in future versions of DNN (not tested in DNN 5 as mentionned)

Ideally...

- DNN should provide a mecanism to create dynamic panes...
- That would enable to create more usable "presenter" controls, such as tab presenter, accordion presenter, where we could add modules to dynamically created panes

I hope this hack can help you out...

Etienne