All savings should be included, including after tax savings and any employer contribution. I can see how employer contribution can be confusing, because you don't necessarily thing of it as income, so you can either count it as both income AND savings, or just savings (the latter makes your savings rate higher). This doesn't really matter much in the end, though.
I also agree with boarder that you should just make your own savings spreadsheet, including income, taxes, expenses, and all savings, and use that to estimate. Just work on saving toward a certain goal, not so much on the "savings rate."