I can't get a pic right now, but only hook the upper bypass fitting to vacuum from the upper side of the blower. As you open the throttle vacuum decreases putting the engine into boost.
The bottom one is for boost, but you would only use it if you have a bypass system like the Cobras. Cobras used some solenoids and the computer to open the bypass at 8 psi if you were at low speed (or something like that), and if you hook it up straight to your boost it will limit you to 4 psi. I had mine hooked up that way at first thinking it would keep me from over-boosting on the street. Just leave the bottom bypass port open, it does not create a vacuum leak.
It sounds like you have everything else hooked up right. All the lines from when it was N/A go to the top of the blower except for the fuel rail sensor which requires boost/vac.