I run one the "Blue Ranger" way. Stock air box with stock tubes, ProDesign plate with K&N, no lid.
You know the little metal fingers on the sub frame that suports the front of the air box. Take a cresent wrench and bend the tabs back out of the way. I bent mine so they are pointed back and inline with the sub frame. Then all you have to do is slip the air box in. It will be suported by the plastic mounting tabs on the air box. It cant slide back any more because of the battery box.
You cant run it bolted in because the tubes will be kinked, cutting off flow. It wedges in tight and it wont go any where.
This is with Keihin 35mm FCR's and a Trinity intake.
It depends on what spigots are screwed in to carbs. There ones that fit the stock boots and ones that fit the trinity intake. The Trinity Intake also moves the carbs down and to the left for a better fit. It also aalows you to have a port matched intake if you have it and the head ported at the same.time.