If you have the option of lengthening your lower arms, keep in mind doing so reduces your lift capacity. May be a non-issue on a large enough tractor but its a big issue on my tiny tractors.
Some lower arms let you attach the lift links closer or further out from the tractor. Closer in gives you more range of motion up/down but lifts less weight, farther out reduced up/down travel but inscreases lift capacity.
Some implements may interfere with rear tires when lifted, requiring you to lengthen arms.
Some implements' driveshaft lengths may require you to lengthen or shorten your arms so that the driveshaft doesn't either bottom out or fall apart during the 3pt up/down travel.
You basically do whatever works, but my default would be as short as possible if you are limited on lift capacity. If you have no real limitation on lift capacity I might just leave them on a longer setting all the time.