Set the charger to lipo. Then tell it the number of cells which for a 11.1v lipo is 3. Some chargers ask for capacity, like 5000mah. The charger should set the charge rate based on what you've told it.
You'll see the charger set a constant charge rate as the voltage increases. For your 3S, the voltage will increase until it gets to 12.6v (a lipo cell max voltage is 4.2v/cell) and then the current will start to fall off while the voltage will remain steady. This is the second part of charging a lipo. When current gets pretty low, charger will signal lipo is fully charged and you're ready to run it again.