From the the Nios,you just want to initiate the counter by start command and then counter (i.e. upcounter) will be starting to increment and then you want MSBs on LEDs, continusouly with the respective values of the counter,right?
If this is correct then it is pretty easy,Just map ur output MSBs (24 to 31 or any bits u want) on LEDs (i.e assign those bits to LED pins).
But choice of number of MSBs depends on clock frequency otherwise you will not be able to see the changes on LEDs ( as it will be so fast)
Ex : for 50MHz clock,you should map from bit (26:31) on LED ( i.e 2^25 / 50M = 0.67 sec).
Like this,you can choose ur bits and increament counter and keep MSBs mapping on LEDs.
Hope you understood.