The Toyota-brand kit has an antenna that mounts inside the windshield. I don't like that because of poor reception when the satellite is "behind" the car. So I also used a roof-mounted antenna. Here's how I routed the antenna cable:

From the top of the roof, the wire goes into the slot that is under the rubber around the edge of the window. Use a thin putty knife (covered with blue tape to prevent scratching the paint) to hold the rubber out of the way while inserting the wire. Use a second device, such as a small sliver of wood, to push the wire into the slot. Do not use metal tools without being covered in tape, because they will scratch the paint. Run the wire all the way around the edge of the window, to a point on the bottom of the window a few inches in from the corner.

From the bottom of the window, there is not a nice way into the trunk. You really don't want to drill a hole there because it would let water into the trunk, directly above the high-voltage battery! I just ran the wire across the 3 or 4 inches to the trunk gasket. That area is completely covered by the trunk lid when it is closed, so it doesn't show. A little tape is useful to keep it from moving.

Then, under the trunk gasket and around the edge to get inside the trunk. The trunk gasket pulls up and reinstalls very easily. I put some electrical tape to cover the sharp edges of the metal at the trunk lip, to avoid problems with cutting the insulation on the wire. Run the wire parallel to the trunk lip for an inch or two at the top, instead of straight up and straight down, so you can avoid sharp bends in the wire. Sharp bends in the wire can reduce reception quality, and eventually cause the wire to fail.

From there, its just a short hop across the metal on the inside of the trunk, to the trim that covers the inside of the trunk. Again, a piece of tape might be helpful. Then its easy to route the rest of the way to the receiver under the front seat. Run it under the plastic trim, not under the carpet, because that route is more protected from damage. The plastic parts pry up easily with the tape-covered putty knife. Just pay attention to all the little clips and inserts when you reassemble.