Opening Project Server 2013 Master Page in SPD:
- Go to PWA site, Site Settings, then Manage Site Feature and activate Publishing Feature. This will enable to select your custom master page later.
- Open SharePoint Designer 2013 and open PWA site using URL something like http://servername/pwa
- Make a copy of Seatle.master
- Make changes to your new master page.
- Go to Site Settings, Master Page (Point 1 makes this option visible) and select your newly created master page.
- Alternatively you can add custom css file separately as well.
Opening Project Server 2010 Master Page in SPD: