seems to me (without much expertise using battery power) that a charging track would solve a lot of problems, given that most locos/tenders are gonna start life with an electrical connection to the wheels. So I'd think you'd need a switch somewhere on the loco/tender that would allow you to make that connection between the charging circuit and the track when you are ready to charge. Perhaps something that is 'remote', like a reed switch that could be activated with an electromagnet, etc. An alternative might be to have a receptacle/plug-in on the bottom of the loco/tender and then a section of bare track over a hole close to the edge of the layout where the 'big hand in the sky' can reach up and plug in the charging circuit (something self-aligning, like an audio mini-plug...).
I recall a recent posting here - might have been GRJ - about using one of the cheap, commercial RC 'key fob' devices to control on/off switches remotely. Might be useful for battery-powered lighting for passenger cars/cabeese.