A place for discussion about skinning and design. Before posting questions here you should review the documentation about creating skins.
I already have a site with mojoportal as cms.
I want to have the homepage to be different than the inner pages. The total structure of the homepage would be different like dashboard etc, where you get the overview of what the whole site is having. This would have different header, etc. For this, can I have a separate masterpage other than the one used by inner pages?
You can use a different skin on the home page. If you enable per page skins in Site Settings then you will see a skin dropdown in page settings.
Hope that helps,