I don't mean to be harsh guys, but if you are asking these questions on a forum then you are SO far away from being ready to start your own affiliate network that you should consider other more viable options.
Forget about the software for the time being. What is your business plan? Who is backing it? Who is providing the initial cash flow? Why would a merchant choose you? Why should an affiliate trust you?
Many affiliates (especially big ones) simply won't join your program until you have a history of trustworthiness and payouts. How are you going to survive in the interim without many big affiliates?
These are FAR more relevant questions to your position than what type of software you will be using.