Treat the clear bra as it was part of the paint. You can polish it, put sealant over it, wax it, etc. Becareful when you polish or wax it. You don't want to get the polish or wax caught between the edge of the clear bra and the car's paint.
If you use the Klasse twins than you don't have to worry about it. It goes on clear with a little residue sometimes if you use the Klasse right.
Another thing that is good to use on your clear bra is Plexus.