The Tenere's headlight switch is wired from the factory so that it's either on main or dip (mainly because it shares the same switch with the X/R that have a single dual filament bulb).
You can get both dip and main to come on together quite easily. Read this:
http://www.xt660.com/showpost.php?p=203832&postcount=8
I'm afraid the flickering when using the flash switch is normal with an HID. They take time to warm up and flicker initially. This is why most cars and bikes with factory fit HIDs only have them for dip.
Wiring your dip beam to stay on all the time will help cover up this problem when going from dip to main and back quickly. Won't help with flashing though.