Ok... *cracks knuckles* here's the deal:
There are two concepts that you need to keep straight in your mind: LHD vs. RHD and driver's side vs. passenger side. These two concepts are not the same thing.
RHD vs. LHD:
Most people in North America are quite unfamiliar with this concept since all our cars are LHD. LHD means "Left Hand Drive"... i.e. steering wheel on the left side of the car. RHD means "Right Hand Drive".
How does this affect your headlights? Its simple. When your steering wheel is on the left, that means you drive on the right side of the road. Oncoming traffic passes you on the left side. When your steering wheel is on the right, you drive on the left and oncoming traffic passes you on the right. When you drive on the right, your headlights are aimed towards the outside of the road, i.e. to the right, and vice versa for when you drive on the left. If it were the other way around, you'd end up shining your lights into the eyes of oncoming drivers.
I'm originally from the UK where cars are RHD, which means they drive on the left. Therefore, their headlights are pointing towards the left. Germany, OTOH, is a country where cars are LHD and they drive on the right. Now, imagine a tourist from Germany driving his car onto a ferry to visit the UK. When he drives on UK roads, he drives on the left, but his headlights are pointing to the right and therefore directly into the eyes of oncoming traffic.
This is where RHD and LHD projectors come into the picture. A RHD projector will shine the light to the left, and a LHD projector will shine light to the right. All this really means is that the cutoff shield inside the projector is oriented in one of two directions.
Now lets talk about driver's side projector vs. passenger side projector. This has to do with the mounting holes on the projector housing itself. The shape of the Bosch E46 projector is assymetrical with a notch cut out on one side. One projector is designed to fit the left side headlight and the other for the right side. These projectors will both shine the light to the same side of the road, regardless of where they're mounted.
The HID Planet Bosch projectors, I believe, are both for the driver's side (or both for the passenger side). But they're all LHD. I don't think they offer RHD projectors.
Now, to convert a LHD to a RHD projector is a matter of loosening a few screws and flipping the cutoff shield over. Operation takes 2 minutes.
Whew... with me so far? Good.
Now for the big question: Is it a show-stopper to have two driver's side (or two passenger side) projectors? A while back there was some information being spread to the effect that, yes, you can't have two projectors for the same side of the car. I believe, however, that several 6club members have dispelled that myth and discovered that it indeed doesn't make a difference. The screw holes line up pretty decently anyway.
So... get the projectors and don't worry about the whole left and right business.
HIDPlanet has only sold the ECE variant of the Bosch E46 projector, to my knowledge, and I've been watching them for over a year now. So, no worries about getting a DOT one by mistake... and this sale's not about to end anytime soon... I don't think. Well, it better not end, cuz I'm thinking of grabbing some of those ECE's myself.
To answer the last question, I need to assume two things: 1. that you're installing the HID system into your low-beams and 2. that you've got an 04 or 05 model car. If this is the case then, yes, flashing your high-beam is an issue. What's been discovered is that when your low-beams are off and you flash your high-beams, your low-beams come on for the brief duration of the flash. This makes flashing your high-beams during daylight hours an inadvisable move since there's potential for damaging your ballasts. Ballasts don't take well to rapid on/off activity. There's no issue, however, when your low-beams are already on, and on the 06's the lighting system operates quite differently anyway so the above doesn't apply.
No one in their right mind would install HIDs in their high-beams
Hope these answers help.