The skins used by the site are located at /Data/Sites/[SiteID]/skins and each skin is basically a sub folder beneath that. Typically [SiteID] is 1 for a single site installation.
Each skin has a layout.master file. You could download this file using the File Manager, edit it locally and then upload it.
So the path will be /Data/Sites/[SiteID]/skins/[skinname]/layout.master
[skinname] can be determined from Administration > Site Settings
be careful, if you put some malformed tag it can break the layout.master and in this case mojoPortal will fallback to a failsafe layout.master file and log an error.
Hope it helps,
Joe