I am all kinds of confused. Being pulled in way too many different directions and too much information online.
This is what I would like, but I am thoroughly confused about how the heck to do it!
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Have my top level domain url redirect (through my affiliate link?).
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Use tracking analytics for traffic going through my redirected domain name. (I would prefer to use Chartbeat, as Google Analytics is sometimes slow, and because it’s sometimes wise to keep a smaller footprint from Big G).
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Customer prospect lands on Clickbank vendors salespage, only it does not have my Clickbank affiliate ID on the end of their URL.
Note: Clickbank does not allow iframes, says it makes tracking unreliable.
Anyone have any ideas of how to accomplish this? Its frustrating the heck out of me! 
Welcome to SitePoint! I’m happy to help you, but I need some more information regarding what you’re actually trying to accomplish.
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What do you mean through your affiliate link? If you’d like to redirect your TLD, most registrars will setup a DNS server and handle this for you as a 301 redirect.
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Regardless of which tracking software you use, I imagine that you’ll want to install it on your target domain, not the redirected one. If you were to install it on the redirected one you’d need to setup a hosting account just to track and redirect users. Furthermore, the user would see a delay waiting for the tracking to load before they’re redirected - not exactly ideal.
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So you have a redirect currently working but it’s not passing your affiliate ID? I’ll need to have an example or at least some more information to understand what your question is here.
Hello,
Thank you for replying! I’m promoting a product which the seller sells through Clickbank, so the affiliate link is a hop link.
I want to use my top level domain name to redirect/forward to the affiliate link, which goes to Clickbank and sets a cookie and redirects them to the sellers homepage.
I do not have access to the landing page because it’s the sellers site.
I can simply forward the domain to the affiliate link, but I was hoping to actually have traffic analysis on my redirected domain so I know where my traffic is coming from.
I would prefer it if my affiliate ID was not shown on the sellers URL, but that is not a requirement.
Bottom line is, how can I redirect www. MySite.com to www. MyAffLink.com, and use Chartbeat or Google Analytics to keep track of who is passing through the page? Currently I just have it as a 1 second meta refresh redirect, but I have read that is bad for SEO, so I plan to change that shortly.
Is it possible?
That clears things up - thanks!
A 1 second meta refresh isn’t horrible for SEO, it’s just not going to help you at all. That being said, both Yahoo and Google treat a no-delay meta refresh as a standard 301. http://sebastians-pamphlets.com/google-and-yahoo-treat-undelayed-meta-refresh-as-301-redirect/
The only way to use a client side tracking system such as Google Analytics is to load the code and then redirect the user. Probably the best way to handle this is to place a javascript redirect just after the Google Analytics code. If javascript isn’t enabled a hyperlink could be displayed instead. However, this isn’t going to provide a seamless solution for your users.
I don’t know that this would work, but have you looked into server side tracking systems like AWStats? Theoretically, you could track the 301 redirect from the server as a visitor. The user would see absolutely nothing and your affiliate ID would be masked. You will just need to confirm that something like AWStats will track 301 redirects.
Regardless of what you do, SEO is a non issue. There’s simply no way to get a site that is a redirect tool into the index and ranking. The fact of the matter is that your website provides absolutely zero content so in the search engine eyes, it’s useless to a user.
If AWStats doesn’t support it, try looking for other server side tracking systems. I’ll be anxious to hear what you found.