There are many different ways to use these settings, along with how you set your rotation, your auto-rest, etc. It all depends on what you are trying to accomplish.
From my perspective, the most important thing you want to do is make sure your best pitchers pitch as many innings as possible (quantity) and as many important innings as possible (quality). I want my weakest pitchers to pitch in mop-up situations, or when I'm resting my lineup, or against certain specific opponents (sometimes interleague, sometimes very weak teams, sometimes very strong teams where I don't think I'm likely to win anyway).
Accordingly I use my TPC and MPC as one tool to try to implement that strategy. I don't want to share all of the details of how I do this - it involves a spreadsheet - but one example is that I set my starters TPC based on the overall number of innings I have in my rotation. For some pitchers, this will mean their TPC is less than the total number of pitchers they could throw based off of their IP/G number. In those cases, I will set the MPC to be the maximum number of pitches they can throw in a game without suffering in-game fatigue.
As rbow923 says, this is a meaningless distinction most of the time, but if at any point I have a fatigued bullpen, it will allow those starters who CAN stay in the game a little longer to do so. Probably no more than 3-5 games in the season; not enough to seriously impact the fatigue of those starters, and it gives me just enough extra leverage in those games when I need it.