You don't need to wait until the batteries are fully discharged. They're lithium ion batteries and don't suffer from memory issues like other batteries. Just stick them on to charge when you've got the time to do it.
I've been using my EVO USB charger rather than the charger that came with the pilot, so I'm not sure about your other questions.
I've been using my EVO USB charger rather than the charger that came with the pilot, so I'm not sure about your other questions.