can I use HAL when the project is linux project?

I need run linux on nios board to use the file system, thus the program project is linux project. The question is whether I am able to manipulate the timer in the nios2 system and how. I can use HAL in Altera NiosII project, but I donnot know how to use the timer in linux project.

The other question is how to generate the position dependent code for the linux project. I didnot find some documents about the memory mapping in the uClinux for nios2.

Thanks!