There's not much one can do to manage the projects shown in Boot Dash:
a) the three hard coded (an not very intuitive) entries in the "Filters" menu
b) the unexpected checkbox in Run Configurations (at least for me, currently not working)

In a) I'd expect to be able to at least select projects not to be shown, or even the possibility to define expressions to match project names.
As for b), that may be a nice-to-have if you fiddle with the Run Configuration -- but certainly not the place where I'd look for it, especially for projects that are not supposed to be run at all (see #605 for a similar sentiment).