MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
The cooling ducts are designed to be vertically adjustable by you (this is why the mount pegs are slotted and there are multiple mount holes in the base). You can lower the duct so that the bottom of the duct is between 1mm and 2mm above the build plate when the nozzle is touching the build plate. In this setup the ducts are directing the air flow directly below the tip of the nozzle at the part.
The best solution to your request for the left hand 5015 fan to get cool air is to use this remix: https://www.thingiverse.com/thing:3481256