Hi Kennie,
Unfortunately, I wasnt able to find any good links to refer you to so I'll just share my limited knowledge and allow others to build on it.
Your netflow stats are sent to devices based on the config on your routers using the command:
ip flow-export destination
I dont know enoug habout Netflow Analyser to say whether setting the BW on an interface provides any benefit. In the case of NBAR it does not.
I dont understand your 3rd point. Please clarify.
If there are protocols you would like Netflow to analyse that your version does not support you can download PDLMs from the Cisco website and install these on your routers.
You can find detail on installing PDLMs here:
http://www.cisco.com/univercd/cc/td/doc/product/software/ios122/122newft/122t/122t8/dtnbarad.htm#wp1075340