Use uClinux on my own design

Best you use a directory under "vendors" for your hardware and software design to allow menuconfig to manage the specific properties of your project. You can use "nios2mmu" as a template by copying the nios2nommu directory below vendors to your own one besites same. In menuconfig -> Vendor/Product selection, you now can select this to manage the configuration files in there and to use the make file it contains, which you might want to manipulate.

Regarding your not NEEK compatible hardware:

either the appropriate driver is provided with the distribution, now you need to do the Quartus design (and thus the ptf file) so that the make process recognizes it. That is why the names of the elements need to be chosen appropriately.

Or there is no compatible (i.e. besites other things: correct names) Kernel driver for that hardware yet: Now you need to create it yourself and take the appropriate steps to integrate it in the make script hierarchy. You need to study the Wiki and the existing script on learning how to do this.

-Michael