It's pretty difficult to grasp everything at once, didn't know there's a difference in behavior. Would something like this work?
http://www.ebay.com/itm/DC-DC-Converter-Mini-Step-Down-Module-BUCK-Adjustable-3V-5V-16V-for-RC-Plane-/371295065523?pt=LH_DefaultDomain_0&hash=item5672e915b3
Very small, 2-3 should provide enough current, efficiency characteristic for this DSN-mini-360 module is listed as 96% max. Not sure if there's a catch I'm missing.
I also ordered a XL6009 step-up board just in case, no idea about what it's noise is. Efficiency is 92% top but with an amp or so of current needed it's better than losing 4% of 5 amps. I feel like worst case I might be able to boost the signal up to 7-9V, then run it through the arduino power jack where the regulator will take care of the noise.
Need to figure out which of these setups will be more efficient so I can choose the battery.