There are any number of ways to cut a mat with a weighted bottom and all of them work. However, the method I prefer, because I find it to be the easiest, and IMO, the fastest, especially if you are cutting more than one weighted bottom mat.
In this example, you are cutting a mat with a 3-1/2-inch weighted bottom. The other 3 sides will have a 3-inch wide border.
1. Set production stops to the width of the weighted bottom (3-1/2-inches).
2. Cut all four sides of the mat at this setting, resulting in a mat with a 3-1/2-inch symmetrical border.
3. Then, using the straight cutter and squaring arm of your mat cutter, and it's measuring stop if it has one, trim 1/2-inch from the top and side borders, leaving the bottom border at it's 3-1/2-inch weighted width.