Batteries should remain in pairs.

[5cardstud]

Most battery chemistries allow serial and parallel configuration. It is important to use the same battery type with equal capacity throughout and never mix different makes, sizes or from different pairs. A weaker cell causes an imbalance. This is especially critical in a serial configuration and a battery is only as strong as the weakest link.
Imagine a chain with strong and weak links. This chain can pull a small weight but when the tension rises, the weakest link will break. The same happens when connecting cells with different capacities in a battery. The weak cells may not quit immediately but get exhausted more quickly than the strong ones when in continued use. On charge, the low cells fill up before the strong ones and get hot; on discharge the weak are empty before the strong ones and they are getting stressed.
This is why it is important to mark your batteries into pairs and always use those two batteries together, never mixing them with others. I use a felt pen and mark mine with an "A" or "B" and so on each time I get a new set.

http://batteryuniversity.com/learn/article/serial_and_parallel_battery_configurations

 

[Wharf Rat]

Well done 5C. Batts get to know each other and don't like new friends. I also mark them 1 and 2 and rotate them front and back (when I remember). The front batt ( I think) works harder.

 

[5cardstud]

Well done 5C. Batts get to know each other and don't like new friends. I also mark them 1 and 2 and rotate them front and back (when I remember). The front batt ( I think) works harder.

I can't take the credit it goes to Serial and parallel battery configurations – Battery University.
This is a very good article to explain the workings of a Series Configuration and it might help people further understand the workings of batteries.

 

[Bovinia]

I mark my sets too but I never thought to rotate front and back. I just put little colored star stickers on each set.

 

[GMoney]

I understand why you are making the point that you are, and I agree that you would not want to use a brand new battery with an old barely functional battery in series as it would most certainly cause the premature demise of the new battery. But, if you have 3 sets of batteries and you rotate them so they all have the same number of charge and discharge cycles, I don't see a problem with mixing batteries. In fact you, I think you might see a small benefit from testing and pairing batteries from different sets which exhibit the closest performance characteristics.

I think the most important thing that can increase longevity of Li Ion batteries is:

Make sure your charger does not over charge. (>4.2V);
Pull your batteries off the charger when they are charged to 4.2V or less;
Always charge drained batteries(Never let them drain below their low voltage threshold ~3V)

Just my thoughts...

 

[Mr.Self_Destruct]

I always mark my batteries as sets. I number them, but I do not mark which is on top or bottom.

 

[BiancaMontgomery]

I always mark my batteries as sets. I number them, but I do not mark which is on top or bottom.

I've been wondering if this is something I should be doing, marking top and bottom (I do keep them in pairs), and if so, should they always stay that way or be switched each use? Anyone have input on the subject?

 

[5cardstud]

I understand why you are making the point that you are, and I agree that you would not want to use a brand new battery with an old barely functional battery in series as it would most certainly cause the premature demise of the new battery. But, if you have 3 sets of batteries and you rotate them so they all have the same number of charge and discharge cycles, I don't see a problem with mixing batteries. In fact you, I think you might see a small benefit from testing and pairing batteries from different sets which exhibit the closest performance characteristics.

I think the most important thing that can increase longevity of Li Ion batteries is:

Make sure your charger does not over charge. (>4.2V);
Pull your batteries off the charger when they are charged to 4.2V or less;
Always charge drained batteries(Never let them drain below their low voltage threshold ~3V)

Just my thoughts...

You could do that if they all had the same number of charge cycles and were all bought at the same time. But sometimes I will use 2 sets more often because they are handy. It would be harder to make sure each set was used the same as the rest of the sets. Also some of my batteries are newer so it's easier to mark your batteries and use them in sets. I have 5 sets of batteries and would spend more time making sure each set gets used the same as the other 4 sets and some of them are different brands and chemistry.

 

[5cardstud]

I've been wondering if this is something I should be doing, marking top and bottom (I do keep them in pairs), and if so, should they always stay that way or be switched each use? Anyone have input on the subject?

I mark mine on the side with a felt pen. It doesn't matter which one goes in first because they work as a set.