I would suggest looking at the Hardware Spec. It lists each pin on the SOM and what the function does:
http://support.logicpd.co...rtalid=0&EntryId=748 Regarding the baseboard, I think I have addressed the sources you questioned and hopefully I can explain how they are sourced:
IO_3.3V_1.8V is driven by U56 which is sourced by the 5V and set to the power level set by M_IO_3.3V_1.8V. M_IO_3.3V_1.8V is driven by the SOM and configurable to either voltage.
uP_5V is connected to 5V through R84, a 0.020 resistor and some capacitors for noise filtering.
SDO_VCC is provided through R223, which is a 0 ohm resistor tied to 3.3V. There is an optional resistor to tie this to R222, but if you populate R222, make sure to remive R223. This would give you the ability to adjust the voltage level on J14 to 1.8 if you have an SD card that is capable of that. Most use 3.3, so that is our default level.
adam