3x3 with 12 plants could be hard to handle, not sure of the size pots, Im guessing around 2L's?
I have the same tent you do, run the fan and filter inside, the carbon filter is around 13 inches by around 9 inch diameter. It has been doing a great job, I'll post a pic below of how its set-up.
With my current setup I have 4, two gallon hempy buckets they are about 12 inches high, by 10 inch diameter. I could let my canopy get to about 36-40 inches from soil MAX, with air cooled hood and fans constantly going.
The inline fan hangs around 12 inches down, so I lose a foot there, & I could keep my light almost 10-12 inches from the canopy.
Pics of four plants in 2 gallon's my journal link below..
FJG