adding to existing insulation
Your first layer of insulation should have the paper vapor barrier facing downward toward your living space. The second should NOT have paper on it. You can buy it that way.
For electrical ceiling boxes with multiple layers of insulation, Cut the insulation on the first layer so that it stops just short of any electrical boxes. For ceiling boxes (lights etc.) as long as they are not generating heat, the second layer can by laid over the top. This will create a small air space around the box. It's really not a problem though unless the boxes are generating heat. Blown insulation usually goes right over them. This goes for water heater vents as well.
The only time you have to leave an electrical fixture uncovered is when you have a recessed lighting fixture that is NOT rated for insulation contact.
The boxes, you'll have to make. Some as simple as old paneling or plywood will work. Get some 1x1's or 1x2 about 12" in length. You'll need these for the corners. Nail the 12" square paneling around it to form a box with the top and bottoms open. Put this over the fixture and voila your good to go. For stove pipes, leave plenty of room around them. Especially keep the paper vapor barrier away from them.