Yes. Of course, you don't plug it directly into the APM, normally, as with an RC RX, normally you plug it into a voltage regulator, like an ESC or BEC.
APM1 also had a variable voltage input option, at a separate point, on the bottom/side.
The new APM2.5+ comes with a new power module that provides the switching regulator, and integrated power monitoring. Take a peek at it at the store or look at Chris' blog post announcing it. See http://store.diydrones.com/mobile/default.aspx#P1148 for details. It expressly states it handles up to 4S.
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APM1 also had a variable voltage input option, at a separate point, on the bottom/side.
The new APM2.5+ comes with a new power module that provides the switching regulator, and integrated power monitoring. Take a peek at it at the store or look at Chris' blog post announcing it. See http://store.diydrones.com/mobile/default.aspx#P1148 for details. It expressly states it handles up to 4S.