Hey Corey, I had my E-Boost hooked up like you did once. There are a few different ways to run the vacuum hoses. IIRC hooking up the port # 3 to a boost only connection got me the most adjustability. Here is a link to a pic of mine. Port #3 runs to the charge pipe in the rubber reducer , just above the positive battery post. The controller is on the fire wall next to the master cyl.
Also check out Turbo Smarts web site. It shows you all the different ways to hook it up.
Here is the link to Their instructions and downloads. Scroll down to boost controllers electronic-- either of the ones that say complete guide.