What should I do if the protocol in ns need to be changed?

[Shimmey]

I am researching the wireless network, such as Ad Hoc, WiFi or WSN(Wireless Sensor Network).
The original protocols in ns need to be changed as my modifys.
But the source code is so hard to understand.
Is there anyone could give me a good way to learn it or can tell me which code files and documents need to be read?
For example, how to modify the TCP's ACK regulation?
Any information will be appreciated. Thanks very much!