I'd leave the battery in. It'll check the charge level, and adjust the charging current accordingly. Li-ion batteries have a finite number of charges. That number is expressed in full discharge/charge cycles. Charging a Li-ion battery 10 times when it's 10% depleted=1 charge cycle.
After many years of using batteries of all types in a professional situation, I've found that batteries don't like being deep cycled. Even the types that tolerate it do better in the long term if their kept as close to full as possible, Ni-Cad included. The worst thing you can do to batteries is overcharge them. I don't think that's really an issue anymore with modern chargers though.
One other thing to keep in mind...Li-ion batteries will be killed if fully depleted. That have circuitry to prevent being completely discharged, but I wouldn't let one sit too long without being put on a charger. It takes awhile for them to naturally drain, but it could end up dropping below critical levels.