You can recharge from any state of discharge. The charger will do all the work. Most all LiFe / LiPo chargers are constant current / constant voltage (CCCV) chargers. They start the charge cycle at the constant current rate you enter into the charger during setup. For a 2 cell LiFe battery the charger will charge to 7.2 volts then the charger will change to constant voltage mode where it will hold the voltage at 7.2 volts and the charge current will taper off until the charge terminates. If the battery just needs just a few MA of charge, the charger will handle that. Likewise if it needs a full charge or anything in between a full and partial charge, it will also handle that.
By the way, other than the applicable voltages and currents, this charge routine is the same for LiFe, LiPo, LiOn and PB batteries. A balance charge will take a bit longer than a non balance charge as the charger analyzes the cells and a bit of charge energy is wasted in the process.
So in short, set up the charger correctly, start the charge cycle and forget it.