After I rode my board, I took off the enclosure because I needed to charge up my 2 Turnigy 5Ah 3s Lipos.
I immediately noticed only one of the 3s batteries was puffy. What would cause only one to puff up? Could it have to do with the fact that I charge them separately as 3s packs? The cells on the puffy one are at 2.8v/cell but when I plugged the not puffy one into the charger it showed 3.6v/cell. I am using an FVT120a ESC with the e-board firmware which doesn’t let you select the LCV
Isn’t this theoretically impossible in a series circuit like the because the ESC pulls from the cell with the highest potential?
Also, now I don’t know what to do. I probably shouldn’t use this battery anymore, but can I just go buy 1 3s pack, or do I have to have a matching set? The set only has about 8 cycles on them 
Many things can cause a puffy battery, manufacturing defects, shorting, pushing the battery too much, unbalanced cells, etc.
Are you sure they were both charged up fully or to an equal state before you started your set?
Maybe the now puffed one was at a lower SoC (State-Of-Charge) when you started and therefore got ruined.
Asking because you said you charge them separately and therefore seems the likeliest reasons I could come up with.
Also, did you balance charge them? Or fast charge?
Where both packs same age?
There’s nothing wrong with charging them separately but you need to always balance charge them.
They were both the same age, and they were both balance charged… kinda. I usually charge them until at 4.4Ah for about 100 minutes. The reason I say about 100 minutes is it charges for 80-90 minutes at like 4.4Ah then I let it balance as it goes between 0-.1 for another 10-20 minutes till I stop it (all the cells are within 0.01V) If I don’t stop it, it goes on for another 30 minutes being completely anal about the cell balance. Yes, I realize that makes me sounds ignorant.
I was under the impression that they will all equal out and drain equally because the battery will pull from the highest cell. Is this not correct?
Is it possible to instead hook up the balance plugs as 1 6s battery so I don’t have to charge separately?
So charge them at 6s, 4.4Ah.
I don’t think that is correct. That’s why it’s so important to charge on balance mode and let the charger run its full cycle until it says it’s done.
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Well shit… Guess I learned a $60 mistake. I guess it could have been worse and blown up, and been a $200 mistake.
So I should probably buy two more packs?
Yes, you can charge them in series as a 6s.
Your battery puffed because you drained it too low. I did that once with 2 brand new 6s packs.
better not go below 3.6v when riding.
The lower your battery gets the lower its voltage goes and the more amps you pull out of it so the faster it goes.
Its like a vicious cycle. and voltage sag makes it even worse because the closer your amp drain is to the battery’s capability, the lower the voltage sags under load.
How can I monitor this when I cant set the LVC of the esc… Just keep an eye on it with the little balance plug meters?
I don’t know what LVC is set to nor how to change it.
get an alarm meter that plugs into the balance harness and monitors each individual cell.
The problem with that is the batteries are in the enclosure so if/when it goes off I can’t really turn it off.
you set the alarm for 3.4v and if it goes off you stop riding
So if I’m far from home I can just turn the board off and push back and it won’t make a peep?
Will it go off from voltage drops while I’m going up hills because the batteries are only 20C/30C
I’ll probably get this basic one from HK because I gotta get my new packs from there.
http://www.hobbyking.com/hobbyking/store/_58827__HobbyKing_8482_Lipoly_Low_Voltage_Alarm_2s_6s_AR_Warehouse.html
If going up a hill sags the voltage below 3.4 then it would go off and you would want it to go off.
The one from hobby king looks good. as long as the alarm is loud enough
I just checked the cells on my puffy pack:
Cell 1: 3.54V
Cell 2: 1.89V
Cell 3: 3.10V
There’s something terribly wrong with this pack. 
This also means it would always be plugged into the pack under the enclosure and it would drain the packs eventually then just go off and scare the crap out of me.
You could run your balance leads to a series adapter cable and run it outside to enclosure and mount the alarm on the bottom of your deck outside the enclosure