Hi Chris,
Welcome to 5 Star.
Well 1st of all when you start a new program you either go with software OR a network, you don't need to do both. I recommend starting off with a network
Linkshare charges around 10K for set-up, CJ charges around 5K but about 3K goes into a deposit toward future commission so it's like money in the bank waiting to be spent. CJ also charges 30% of affiliate payouts or $500 a month (whichever is greater). Last I checked, so this info could have changed.
The networks I recommend cost much less. (Actually if you had a big brand and big budget, then I would recommend CJ.) But assuming you don't, I would look at
ShareASale Many affiliates prefer them over CJ. It's a much smaller network but still has lots of strong affiliates. Set-up is only 350. Then they only take 20% or min 25 for network access fees. They still serve your banners, pay your affiliates and do all the things the CJ network does.
Another good option is
ShareResults . They are one of my 5 Star clients and they really go above and beyond for both their merchants and affiliates. Their pricing is about the same as Shareasale. They are both really good options!
Hope this helps at least point you in the right direction.
Let me know if you have any other specific questions as you go along!