Move data from NIOS to hardware and then back to NIOS

You might have an easier time using this instead: http://www.alterawiki.com/wiki/modular_sgdma

Assuming the UP IP core has an ST port into the core and another ST port coming out of the core then you could just slide it in between the read and write masters and do the transfer all in one shot. Just look at the Nios II software code to find out how to setup a descriptor.