The instructions for the Roadstar rear fender are included in the saddlebag bracket instructions pdf
I was thinking about the pros and cons of not including the bobbed stock fender under the Bad Dad fender and looking for pics last night. The fender base appears that it would be more sturdy than sitting the BD fender on the swingarm but I trust that they have adequately stress tested their product. I also may have found one on their website with the fender base.
Another consideration is that the edge of the BD fender runs parallel to the ground instead of curving under the seat. This would mean a lot more rear wheel would show from the side with only the BD fender, above the "splash guard", than with the fender base. I did not realize this and got a white donor R* fender to "bob". So, a little of the white fender shows under the seat now on each side. This winter I'll have to paint those small fender areas either black or black cherry.
As Yogi mentioned, and as seen on the instructions in the link above, they suggest adding the bobbed fender unless they have revised the instructions. Did you tell them you plan to run two up?