On their documentation page, Adafruit offer a tutorial for using it with 2s li-ions. However that also required a 3pdt switch, which would have to be manually thrown. Since in my project I will not have the indicator lights visible, I can easily see my self or others forgetting to flip it and either wonder why it doesn't work, or wonder why it's not charging.
The only thing I can think of using is a 5V 3pdt relay, that would have the coil terminals connected to the DC-IN terminals of the charging board (the input power would come from the micro USB port) so that when the charging cable is plugged in, it would automatically switch to charging mode. Unfortunately a 3pdt relay is rather hard to find, especially in small sizes.
Is there another option I'm not thinking of? Or can someone point me in the direction of a small 5V 3pdt relay rated for at least 1 amp?