I only have one controller but two batteries for it, I use one until it shows low on charge then I swap it for the other, wait for a few days then recharge it while the other is being used.
This also gives me the option when out flying should my operating battery start to fail I have a back up ready to go.
Replacement batteries are about $35 to $40, from most vendors.
From what i understand the storage charge should be about 60% with lith's.
I charge mine with an Imax B6 V2 charger and it has a setting to recharge a low battery to a storage charge.
The B6 can charge both Lith-ion and Lith Poly, quite a nice feature.
If you are just using the stock OME charger then I might suggest you watch your controller battery state until it gets down to 2 bars, then swap to the other battery.
At least this way you get to use the battery, and all batteries have a shelf life, might as well use it while it's still good.