Building uClinux using Nios 3.2 / Microtronix 1.3

I am using Nios I and Microtronix uClinux 1.3 for a hardware design in which the memory map differs from that of the Altera Cyclone reference board.

I cannot get uClinux to run out of flash on my board. What, and where, do I need to make changes in order to build the Linux.flash and romdisk.flash files to suit my custom memory map so that Linux will start and run properly?