I have a 99 civic si b16a2 and an external waste gate where do I plug the 2 vacume hoses into? Also how do I hook up my manual boost controller?

 

Don't worry about the "top" hose. Hook up the side hose to the MBC to the turbo (or whatever boost reference you are using)

I *believe* you only use the top hose if you are running an EBC. I've never had to worry about that b/c EBC's are for ballers.

 

Correct on the top port of the external gate being for EBC's.

So..

Vac/boost source ----- MBC ------- lower/side nipple on the wastegate