Are you using pencil or marker? Marker shows up better and if you do use it no one will be thinking to look for the dots anyways. Plus the "marked bills" never should be handed out so your spectators should never even see it.
My bad I just rewatched and I guess the "marked bills" do get handed out. Shouldn't be a big issue if someone sees the dots though since it's basically irrelevant to what's going on.
In the video he mentions holding the bills at an angle to where they will naturally just kind of fall away from the gimmicked bill. I think this is what you are referring to.
