The best recommendation I have if you want to use a custom skin on a custom page that inherits from mojoBasePage is as follows:
yes it needs to be a standard mojoPortal skin and it needs to be located in the /Data/Sites/[SiteID]/skins folder like all other skins.
you can set it programmatically to the chosen skin from code in OnPreInit like this example code where I am forcing a custom page to use the artisteer-greenlagoon skin.
protected override void OnPreInit(EventArgs e)
{
base.OnPreInit(e);
MasterPageFile = "~/Data/Sites/" + siteSettings.SiteId.ToInvariantString() + "/skins/artisteer-greenlagoon/layout.Master";
StyleSheetCombiner style = Page.Master.FindControl("StyleSheetCombiner") as StyleSheetCombiner;
if (style != null)
{
style.OverrideSkinName = "artisteer-greenlagoon";
}
}
Hope it helps,
Joe