The hwselect script will prepare the headers of the memory and io port maps of your board. You must run hwselect before compile the kernel.
In uClinux-dist, you will run "make vendor_hwselect SYSPTF=/path_to/your_sytem.ptf" instead of "make hwselect".
If you change the ptf later, you have to "make ... clean" the kernel dir. Then run "make ... hwselect ...."  again.

If you use Altera Nios II dev boads, look for the ptf and sof in dir, altera6.1/nios2eds/examples/verilog/  ,
eg, if you use Altera CycloneII NIOS dev board with 2C35, the ptf file is
/opt/altera6.1/nios2eds/examples/verilog/niosII_cycloneII_2c35/standard/std_2C35.ptf,
and the sof is standard.sof . The ptf must match your board and the sof.
If you use DE2, look in DE2_System/DE2_demonstrations/DE2_NET/ nios_0.ptf and DE2_NET.sof .

Here is the hwselect of std_2C35.ptf,
--- Please select which CPU you wish to build the kernel against:
(1) cpu - Class: altera_nios2 Type: s Version: 5.11
Selection: 1
--- Please select a device to upload the kernel to: (nothing listed to select if you don't have cfi flash, this is OK)
(1) ext_flash
Class: altera_avalon_cfi_flash
Size: 16777216 bytes
Selection: 1
--- Please select a device to execute kernel from: (you have to select sdram here)
(1) ext_ssram
Class: altera_avalon_cy7c1380_ssram
Size: 2097152 bytes
(2) ddr_sdram
Class: ddr_sdram_component
Size: 33554432 bytes
(3) epcs_controller
Class: altera_avalon_epcs_flash_controller
Size: 2048 bytes
Selection: 2

When you compile the kernel, file linux-2.6.x/include/nios2_system.h will be generated. It contains the memory and io ports address of your board.