There are 2 option we can follow to do this.
1. First one is modifying existing theme. This will be update safe. Here are the steps to do that.
a. Copy Masonry layout (choose that one you never wish to use without customizing) to your theme.
b. You will get the new path of the theme.
c. You can edit those files as per your requirement.
d. While creating shortcode select the layout you have customized.
2. Creating Custom Theme. Need to reset some settings after update
For this please check video here. (It is uploading now. Please check after 30 mins) http://youtu.be/zR9MKbIbacM
However, i prefer using Option 1. Because, there is less chance you are going to use all the 4 layouts in a site. So customizing one won’t make much difference.