Stacking batteries is discouraged because while it can be safely done in the Vamo, the steps that must be taken to do it are extensive and the penalty for breaking the rules can be disastrous. Please understand that it increases the risk factor so adherence to a strict protocol is absolutely necessary.
To do it, 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 one of the two can never be used without the other, nor can either ever be used in conjunction with another that is not from the same married pair.
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.
Even though the Vamo has the protection circuitry that the other mods don't, that doesn't mean something can't go wrong. That's where the safer chemistry of the IMR cell comes into play.
The dual 18350 capability is a small advantage that the Vamo has over other systems. The Vamo detects the higher voltage and adjusts how it manages power accordingly. The device will display "Low V" in stacked mode when the tested voltage falls below 6.4v. The only advantage you gain is the theoretical abililty to run at higher loads for longer times, but at the expense of battery life. Real testing of the Vamo indicates that those theoretical gains aren't possible at the higher end of the scale because of the amperage limitation of the device (5.0a). The "safety ceiling" of the device's circuitry doesn't allow the computed power output to be obtained from the higher voltages available in stacked mode.
Example: Assuming a 2.0 ohm coil and max current output, 2.0 ohms x 5.0 amps = 10.0 volts, which is well above the voltage limitations of the device. The power output would be 5.0 amps x 10.0 volts, or 50 watts. Again, well above the threshold of the device and not achievable.
Other mods are not designed for stacking batteries at all, and doing so voids the warranty. Most regulated mods cut off when battery voltage drops below 3.2v. That is 1.6v per battery, which is well below the lowest discharge voltage of the lithium ion chemistry and it will either kill the cells or cause an unfortunate incident. Just because the Vamo can do it doesn't mean that you should try it with other devices that look like they'll take it.
Unregulated mechanical mods can achieve the theoretical limits, but doing so will put such a drain on the batteries that an unfortunate incident is a near certainty sooner or later.
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 high quality IMR or hybrid chemistry 18650 in there and let it ride.
I have two Vamos. I've never stacked 18350's in either of them and I don't recommend it. Just too big of a hassle, not enough benefit for the increased risk and it's not cost effective because even the best 18650 cell costs less than two 18350's. It's just not worth it, even though it is possible.