Only about 2 qts drain out of the pan, I'm assuming that the rest of the oil is in the cooler. How to fully drain and refill without causing air in the oil lines?
thanks in advance for any advice/assistance in this matter

 

You should get way more out than 2 quarts by draining the pan, unless the oil level was seriously (and dangerously) low. More like a gallon or so.
I never bothered with draining the oil from the coolers and have 146,500 miles on the original engine, so it should not matter.

 

If it is a 2009-2011, changing the oil on an unlevel surface will cause this. It will also be made worse with a quick change oil valve installed.