I can tell you how the C-9000 does it for new batteries.
1) Discharge the battery fully, just to be sure. If it's not a low self discharge battery, it will probably only have a 10% state of charge anyway, so this happens very quickly.
2) Put the battery in the charger and enter the battery capacity. It can then charge at 0.1C on a timer to what should equal the full capacity.
The key there is having a mode where you can enter the capacity of the cell and let it charge to that capacity. For example, say I buy some brand new 800mAh AAA cells. I'd first use the discharge cycle to run them down to empty. Then, I'd put them in the charger and program the charger to see they are 800mAh cells. It then charges at 80mA for 15 hours on a timer. The reason it goes for 15 instead of 10 is because a huge amount of the energy is lost as heat when you charge that slowly.
Likewise, if you put a 2700 AA in there, you'd program it for 2700 and it would charge at 270mA for 15 hours. Same deal; the key to doing a slow charge is that it needs to be completely flat before you start followed by running on a timer since it's virtually impossible to detect the voltage change and temperature spike that you'd look for on a 0.6 to 1.0C charge rate.
I think the bottom line here is that if your charger can't do a timed charge, I'd personally just run the battery to 0.9V discharge to make sure it's flat, then charge at 0.5 or 0.6C rate, which is around the slowest rate that you can charge and reliably detect the voltage or temperature peak.