Which Macbook Pro USB port should I use to charge an iPad?
You can use either port, the limitation is that only one USB port can provide this higher power level. If you try and charge two iPads at the same time, only one will get provided with the higher power level, and the decision as to which is made on a first-come-first-served basis.

Edit to Add: I forgot to mention that the article says Macs with more than two USB ports may be capable of powering multiple ports (but not necessarily all) at this higher power level. Unfortunately they don't give any further details.

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