The best way to is place the drive box away from the chip making area.
Seriously that is a good question. It is designed to draw air in from the bottom vents and exhaust out the top vents so there is a 'bit' of air flow that discourages chips from settling in the top vents. In fact there is an 'attic' floor that serves as both a secondary area to mount components as well as a thermal management device. It insures that the cool air drawn in the bottom of the case can only exit via the power supply fan or by convection past the G540. I did several 'torture' tests driving four steppers and adding several amps of static load to the power supply (to load it down). After several hours the case temperature was in the 95~97 degree range in a 70 degree room. It also maintains it cool in my 95 degree shop. So there is the proper amount of airflow through the case to keep it cool without adding lots of additional fans (that you often see in other cases) that only serve to encourage the inclusion of more chips and dirt.
Any enclosure that is vented (and almost all are) will have the same concern. I'm mounting mine on a shelf under the table that the mill sets on. The PC will be just below that. Some folks have there mills enclosed to prevent such issues as well. What ever case you use to house your drive components it doe spay to consider how to protect it from damage.
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Happy Machining!
Jeff Birt - Soigeneris.com
Proud Dealer of Taig, Precisebits, Gecko 540,
SmoothStepper and A2ZCNC products.