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It is recommended that you Don't run down until self power down as it has been proven the cause of some phones becoming unresponsive to charging or powering up (black screen of death). You only need to run down to the Low Battery warning, since that is the point where the bottom level trigger is set. There's a reason why the low battery warning comes on so soon, and that's so you have time to complete your work before you power it down manually, and/or until you can find a power source.
As for charging to 100%, that's best done with the power off as it allows the charging circuitry to get an accurate reading of the charging process and determine accurately when the battery has reached capacity. Once it reaches 100% and shuts down charging the top level is set. As you indicate, this should be done once every 1 to 2 months to keep ths battery properly calibrated to the level indicator.