Hello!
well for this
"Is the air intake connected to the throttle body"
Yes... engine sucks air through intake manifold..and air intake is connected to Plenum in which TB is.....!
Well After Itbs.....it depends....if u r gonna run Open ITbs...then use Individual Air Filters directly on those....!
Let me post some pics to make it clear 
A STock Engine showing Air Intake Setup..u can see it after TB...

There are ITBS OPEN ITbs..so no need of Air Intake....it all takes individually....! In pics Below..its running Open...u can place Filters on them...!

Like This...Open Itbs with Filters

ITBS Intact In Plenum SUcking Air From Intake piping

Hope This Helps
Regards
