Yes that's the best place to spray it because it goes through the entire system. It's just a little difficult getting to that area. It will leave a slightly sweet smell coming out of the vents. For the guys who drive very short trips this is the best way to eliminate mold and bacteria from the system.
I had to get to that area earlier this year to clean out some leaves stuck near the intake. I thought it was pretty easy, the only troubling part was removing the passenger side cowl without cracking it. The factory seal was very tight.