how to access the jtag uart in the nios code

Perhaps what you're referring to the actual hardware implementation of the NIOS. There are three variations of the NIOS (economy, standard, and fast). Perhaps you're indicating that the contractor created the "economy" version of the core. I believe if you look in the "system.h" file inside your BSP or System Library there is a line similar to the following:

#define NIOS2_CPU_IMPLEMENTATION "fast"

This indicates which core was chosen. Consequently, the "economy" core is very slow with regards to it's MIPS performance.

With regards to the settings I previously mentioned. They are configured in your BSP or System Library settings.