I use to stack batteries in Vamo V5 all the time. Never had a problem, but it becomes a pain to track with 2 or 3 or more sets of batteries.
1) Buy all the 18350 sets you plan to use at the same time
2) Label your batteries in pairs. i.e.: 1A 1B 2A 2B etc.... These pairs are now married and are only to do everything together.
3) Always use the same pair at the same time.
4) Always charge the same pair at the same time.
5) Measure the voltage of both batteries after charging. They need to be the same voltage, or very very close. If they are way off, one will pull from the other and over discharge the lower one possibly causing an overheat condition.
6) Rotate the batteries everytime you use them after a charge. If you put them in your mod 1A 1B, the next time you put them in you would go 1B 1A.
If either battery shows signs of wear, replace both. Never mix and match pairs.
I did it because I could, and followed the above with no problems in a mod that supported it. Then it got old and went for 18650's for simplicity. Much happier now.