Where to put a power switch, how to charge a battery

Where should I connect the switched power supply?

I'd suggest that you solder onto the back of the connector... See the next point...

connecting the battery to VBat would circumvent the fuse, right?

Yes, it also means that if your battery voltage is less than 5v (which a LiPo will be) and you plug it into USB you'll end up over-charging the battery (even without the charger IC), which could be very bad news.

MAX1551 ... Doesn't that mean that the board will always be on during charging?

Yes - I think you'd have some trouble switching it around so you could keep the Espruino off while charging.

Is there a specific reason you're worried about the Espruino being on? When it's in Deep Sleep it draws virtually no power (0.03mA) so there's actually not much of an issue keeping it on and having a 'soft' power button.