You should not modify the mojoPortal source code at all, if you upgrade you will lose changes.
The site uses the layout.master file from the skin folder at /Data/Sites/[SiteID]/skins/[skinname]/layout.Master
However the layout.Master file in every included skin inherits from App_MasterPages/layout.Master.cs
This code behind handles assigning css classes to the divCenter based on whether each of the panels has any content or menus in it, so it facilitates automatic column layout from 1 to 3 columns.
Nothing stops you from making a new layout.Master that inherits from your own code behind file but then you lose the built in column layout feature.
Best to just create a custom UserControl and declare it in the layout.master file of your skin without touching the C# code in layout.Master.cs.
Hope it helps,