First of all, are you using the light head's internal flasher or are they set up to an external flasher?
If it's internal and the unit doesn't have a primary/secondary flash pattern selection this will pretty much be impossible. Otherwise, hook up the primary flash pattern (set to steady burn) to a relay that's activated by the brake lights and the secondary to a warning pattern to your control head.
If external and the flasher doesn't have a primary/secondary you can still make it work. Since the light is already set to steady burn for the flasher, simply tap into the power wire between the flasher and each head, use a diode to prevent backfeeding on the line from the flasher, and connect the other line to a relay that's controlled by the brake lights.
Hopefully someone can post a photo or diagram of what I mean because my work computer is giving me hell right now.
Oh, final option, buy a external flasher (whelen ULF44 comes to mind) that has a brake light override feature.
