i often make sure to amplify files to a level where they can be easily heard before saving them when i use audacity.
there is a nice little tool in the new beta
http://audacity.sourceforge.net/download/beta_windows under effects>SC4.
using that you can amplify the sound of files beyond the clipping range without it clipping, so you can use it to make those lines you want to sound like you're shouting do so.
hope that makes sense.
but yeah there are plenty of ways to match audio up in loudness, the best advice is to just amplify it to the point that you can hear it without a doubt and no real matter if some are quieter than others, if all can be heard then that's all that really matters. In that case people over the phone most likely wont realize at all that there is a difference between overall loudness in some lines because when people talk over the phone they do get louder and quieter all the time.