basically you get the footprint of a bga part and turn it into a throgh hole footprint (ie drill all the way throgh),
you then design the rest of the board so that the 2 RAM BGA parts connect to the correct pins so basically the RAM chips are off to the side and are sitting next to a footprint copy of themselves that have holes going throgh the pcb
now you unsolder the ram and solder small pins or snipits of led/resistor legs to where the old ram was, the idea being that this lines up with the bga foot prints that are throgh hole
you then place the pcb you made over these "pins" and feed them throgh, soldering and cliping off the excess as you go
nice and easy however it might be easier to just unsolder and resolder the bga part, software wise you have to identify the boot parameters and modify them as the intel PXA chipset will need new size /bank parametors for the new ram chips (nothing a binary grep wont find)