Flash the boot like any other roof penetration, and snap the tube into place—just make sure to align the hole between the ceiling joists...
Step by step:
Mark the roof between two ceiling joists
Turn the flashing piece upside down and mark the circle on the roof.
Cut the hole about an inch larger than the circle.
Nail the flashing to the roof deck, weaving it into the shingles. Use 4-5 nails per edge for wind resistance. Note: in areas with higher rainfall than LA, tuck the upper edge of the flashing under the roofing underlayment, shingle-style.
Spread roofing cement along the top and side edges of the flashing.
Continue shingling around the flashing.
Apply silicone sealant to the light tube's interlocking collar.
Paint the exposed metal black or whatever color you desire.