POE is not supported on the BeagleBoard-xM. If you want to do it externally and covert the 48V to 5V and then use that to power the board, you can do that.
There are two working USB ports, one the OTG port with the small USB connector and the one that goes to the HUB which gives you four USB ports. USB3 has not been used. Why do you need more than 5 USB ports?