Andy, I'm no expert at smoking...yet
but I do know HVAC which includes fans, static air pressures and such.
How tight do you plan to build your enclosure?
What type of exhaust venting are you going to use?
How many cubic feet per minute does the ATC you plan on using draw?
As a rule with the info you have supplied so far, I would say the ATC intake should be on the outside. You want to create a slight positive air pressure within the enclosure.
There is a trade off being colder air in will = less BTU's out. Depending on outdoor air temp, you my notice an increase in your fuel consumption on colder days.
There is another option depending on your design. An outdoor intake with a small damper on the inside in series with the tube. This would give you the option to adjust or mix some slightly warmer air into the feed. All you need is a very slight positive pressure within the enclosure to achieve proper venting/exhaust.
Good Luck with your project!