Hi Aaron,
I strongly recommend against companies developing their own in-house tracking. Affiliates don't trust it and like the comfort of using software they are familiar with. There is NO WAY you can build software that has everything and does as good a job as software that's been out the for years, has been through beta testing, then used and improved via feedback from thousands of affiliates.
If cost is the issue there are lots that are so affordable there is no way you could pay programmers less. Think of it this way. Why in the world would you want to pay your programmers to build a custom word processing program and try to get all your employees to use something so foreign and different than what they are used to, when you can just buy Word?
Don't know why you wouldn't just buy idevaffiliate or something for $100 and be done with it???
That said, I'm not understanding how you can build it if you don't know the basics all affiliate tracking programs need to have. I suggest you and one of your programmers go through the idevaffiliate demo together and review all the different reporting options. Here's a list of features and logins to the admin demo are at the bottom of the page.
iDevAffiliate - Affiliate Tracking Software
FYI I'm not saying idev is the best, I don't really have a personal fav low end tracking solution. It's just one of the lowest cost, well respected ones I know a little about.