How can I communicate Serially with an Atmega328

Even easyer than Lefty's suggestion:

Use TinyISP instead of ArduinoISP.
With that you don't need any swapping around wires, just leave everything as it is when programming, and open the serial monitor as you are used to.

TinyISP:

https://github.com/Coding-Badly/TinyISP/zipball/master

TinyKnockBang library
https://github.com/Coding-Badly/TinyDebugKnockBang/zipball/master