I have often used Krylon primer on clear plastic pieces where it would need to be masked off and painted. Works fine. Only hard part is that it often needs to be masked on both sides, especially in places like cockpits. Getting the inside and outside masking in register can be challenging.
Once primed paint like normal. Oh, and seal tape, as if there is any bleed-under, removing it will undoubtedly dull or scratch transparent panel. Use a good tape like Tamiya and seal with Glosscoat.