Stacking batteries is discouraged because while it can be safely done, the steps that must be taken to do it are extensive and the penalty for breaking the rules can be disastrous.
You have to make absolutely sure that both batteries are brand new and of the highest quality possible. Both must be from the same maker.
Both batteries must have identical nominal and nearly identical actual capacities. Just because they both have 700mAh on the label doesn't mean that they both have actual capacities of 700mAh. There are variations in the manufacturing process and the batteries could have significant differences between them, even if from the same manufacturer. That's why AW IMR's are so highly recommended. They perform as closely to spec as can be.
The batteries must be married and never be separated, until death do them part. They have to be labeled and can never be used without the other.
They have to go on the charger at the same time and come off at the same time. They have to be rested for an equal amount of time and have to be tested with a multimeter once they've rested.
They have to be rotated in position. Battery A goes in first one time. Battery B goes in first the next time.
Forever and ever, Amen.
Furthermore, the increased risk associated with a stacked pair of 350's is not worth the additional cost. A single 650 cell of highest quality still costs less than the highest quality pair of 350's cell. You pay more for the batteries, and increase risk? Is that wise? Your call.
Also, when stacking the batteries, you get increased voltage. But both cells will discharge at (hopefully) the same rate, so there is no increase in capacity. Two 700mAh batteries do not equal 1400mAh.
You can stack'em if you want, but unless you're OCD enough to keep up with all of this, it's best to just stick an 18650 in there and let it ride.
