Hi Stefani -- Most of my affiliate programs are through Clickbank, but I use this great Excel Spreadsheet software that lets me keep track of my costs, profits and ROI.
I should also qualify this by saying that I do most of my affiliate work via pay-per-click.
So, with that in mind, this program does a great job of keeping me organized and on top of what is making money and what is losing.
Each day I just log in to Adwords -- pick up my stats on each campaign I'm running -- then log in to Clickbank and see what the sales are for the day and plug them in, and I have a running update on each of my affiliate campaigns. It keeps track of each campaign, and also keeps a running total of all campaigns for each month.
It's called "Campaign Tracker" and it has proven itself over and over again for me.
http://youcould2.rpgun1.hop.clickbank.net
That is an affiliate link, by the way.
I hope this info will help you.