Clickbank, Multiple Passwords, and Affiliate Commissions?

I'm currently writing an Ebook and have been looking at all of the publishing options.  

I'm very impressed with this software so far but I'm a little confused with how the multiple passwords work as far as paying affiliates over at Clickbank.

Normally when a person buys an ebook at Clickbank the affiilate sends the traffic to a sales page and the customer decides whether to buy or not..this is pretty straightforward.

But let's say I have 10 different passwords needing 10 different sales pages.  From what I understand the way to use this system is to not have the potential customer buy the password outright but to first download the software.  

So my first question is:  Does one just have a single sales page that affiliates send traffic to - the potential customer downloads the software to their hard drive and then from within the Ebook the customer clicks to get a password and they are THEN sent to one of the 10 sales pages?  They are lastly sent to one of ten different "thank you" pages, all with different passwords?

Finally, how does Clickbank track all of these sales pages, thank you pages, and in the end pay a commission for the sale, when the customer originally just downloaded software.  Does the cookie track all the way through?

I ask all of this, because I plan on using affiliates almost exclusively to sell my products and I think many will be confused with this setup.

Thanks in advance,

When a person clicks on an affiliate hop link this sets a cookie on the user's browser, which I think last for a couple of months

If the person later buys from the merchant, the cookie is spotted and affiliate commission issued.

If a person returns to the merchant's site long after the initial click, e.g. bookmark or clicking on password-page in ebook to sales page, the cookie is still there