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Is it safe to charge a lipo pack that is already run down some, or do I need to discharge it compleatly first? Also what is the best way to store them, and is there any maintence to do to them while in storage? Winter is coming and I'm not sure what to do to them as the lipo packs will not get much usage while there is snow on the ground.

Storage: If you don’t plan on using your lipo pack for longer than a week, store it at 50-60% of the pack’s rated capacity. Make sure to cycle and/or balance your packs at least once per month since leaving them on the shelf for a prolonged period of time can cause the packs to get severely out of balance or even go dead.


more can be found here
http://www.maxamps.com/lipo-care.php

So how do I do that 50% charge? The charger is a TRITON EQ. Lets say the battery is a 3c 4000mAh, do I just program the charger as if the battery is a 2000mAh? Will the charger stop at at the correct time if set up this way? I'm trying to protect my investment and there is so much info out there it is all very confuzing

We will just have to run them once a week thru the winter in an under ground car park so you wont have anything to worry about

Never thought of that

Check if the charger has a storage function. If you tell it you have a 2200mah battery it'll just charge it at 2.2 amps instead. If you don't have a storage function you could fully charge it then discharge it and watch until its drained 1600mah out of it for a 4000mah battery.

Personally I just leave them with whatever charge they have after a race, or if I didn't use them on a race day leave them fully charged. Haven't had a problem. Even have a trakpower 4900 thats been sitting for about 5 months on a full charge and is still holding the full charge.
Apparently SMC's don't like to be left charged for more than a day though

use a voltmeter guys..
4.2 volts per "s"cell is full charge
3.7 volts per "s"cell is 50%
3.1 volts per "s"cell is empty

so 2x for a 2s and 3x for a 3s... and so on...

Just store them fully charged, and remember to charge them every few months.