Hello,
unfortunately there“s no way to save the custom colors between design sessions. It is not even possible to replace the existing layout templates or create a new one. The only chance (even though a small one) is to create XML Template Parts which will give you something similar. Specify an XTP. The XTP can then be dragged into your various views to prepopulate with any layout you want. Of course, you need to create the XTP first. You can use the designer for that. XTPs are great for consistency colors and layouts and reduce form development time.
Hope that helped.
Regards,