The hwselect script will prepare the headers of the memory and io port maps of your board.
Change to the uClinux-dist directory
make vendor_hwselect SYSPTF=/path_to/your_sytem.ptf    # this is instead of make hwselect

If you change the ptf later, you may have to make clean the kernel dir.
Then run make vendor_hwselect SYSPTF=/path_to/your_sytem.ptf again.

If you use Altera Nios II dev boads, look for the (any) ptf and sof in dir, /opt/altera8.0/nios2eds/examples/verilog/  ,
eg, if you use Altera CycloneII NIOS dev board with 2C35, the ptf file is
/opt/altera8.0/nios2eds/examples/verilog/niosII_cycloneII_2c35/full_featured/NiosII_?cycloneII_2c35_full_featured_sopc.ptf ,
and the sof is  NiosII_cycloneII_2c35_full_featured.sof . The ptf must match your board and the sof.
If you use DE2, look in DE2 support CD, DE2_System/DE2_demonstrations/DE2_NET/ nios_0.ptf and DE2_NET.sof . (look for *.ptf, the filename may change)

You should select a Nios2 cpu, and sdram/ddr/ddr2_sdram. Your memory size should be at least 8MB.

Here is the example of NEEK,

  RUNNING hwselect

--- Please select which CPU you wish to build the kernel against:

(1) cpu - Class: altera_nios2 Type: f Version: 7.071

Selection: 1

--- Please select a device to execute kernel from:

(1) ext_flash
        Class: altera_avalon_cfi_flash
        Size: 16777216 bytes

(2) ssram
        Class: altera_avalon_cy7c1380_ssram
        Size: 1048576 bytes

(3) ddr_sdram
        Class: ddr_high_perf
        Size: 33554432 bytes

Selection: 3

--- Summary using

PTF: /home/hippo/boards/ocm/cycloneIII_embedded_evaluation_kit_standard_sopc.ptf
CPU:                            cpu
Program memory to execute from: ddr_sdram

--- Settings written to /home/hippo/nios2-linux/uClinux-dist/linux-2.6.x/arch/nios2/hardware.mk

When you compile the kernel, file linux-2.6.x/include/asm-nios2/nios2.h will be generated. It contains the memory and io ports address of your board.