Using different jtag connectors for HPS and FPGA

Hello All,
We have our own custom board with SoC5CSEA and DDR3 MT41K on it.
The SoC is connected to MTQL512 QSPI.
The FPGA and ARM are having there own JTAG connections.

I want the ARM processor to act like a normal microcontroller. e.g. i want to run it with out the FPGA. The ARM should be able to initialize it configuration registers for the ADC, for the PLL, for the BUS interface etc etc.

Is it really possible?
can i run both FPGA and ARM processor independently?

Is there any tutorial available for such type of bare metal applications?

Hamid Saeed