I'll try to answer the second one since I've never swam the asyn ram waters.
Depending on how you want to implement your system, different designs with the NIOS II processor are possible. If you are offloading DSP type calculations then I recommend using custom instructions with registers that you can configure. So you would pre-configure these registers then start using the hardware as a whole as custom instructions. If you are simply programming a filter that is implemented in DSP hardware then I would create external hardware that programs the DSP multipliers on the fly.
As you can see I'm staying general to avoid a lot of typing before I know more about the system. Could you explain what the NIOS is doing, is it just reading the output from a filter (so data feed directly into the filter), what data rate you need, etc.....