Between the two processors there’s a direct UART serial connection which is always ON. Beside this there's an USB OTG connection used, for example, for the ADK communication protocol between the iMX6 running Android and the SAM3X. For more details and other connections modalities: http://www.goo.gl/O3EnI
PWM, Communication and Digital I/O pins can be controlled from the SAM3X (Arduino) as well as the i.MX6 (Linux). Each pin can be individually configured to be driven by one or by the other processor. Configuration is done via software.
At the moment, we don't have certain data about consumption, since we are running UDOO's prototypes. The iMX6 ARM Cortex A9 assures lower power consumption than older ARM CPUs, like for example the ARM11.
UDOO features a standard barrel jack with 5.5mm outer diameter and 2.1mm center pole diameter. The AC to DC adapter provided with the kit reward is a 12V @ 2A that provide 24W, which is enough for UDOO itself and other hardware plugged to it (eg SATA HD or Arduino shields).