You would hold down E to charge it yes, you'll hear beeping which will tell you it's working. Make sure you're not holding the PDA or the watch, it should come up with a message when you look at the charger. I BELIEVE so long as you haven't let all 3 gens die it'll let you charge even if one or two are down. Don't take my word on that though.
As for night 4, there is none yet however from what I gathered they are making night 4, after which they're going to work on the remaster. I myself am not sure when Night 4 is expected