I'm planning to use Aweber (or perhaps any other autoresponders) in the below sequence
Lander -> Capture email -> Aff link
The email capture will be a popup box.
Eg: Click here to access! --> Pop Up to enter email -> Click Next
However, where and how do I implement the /click link to properly track the campaigns?
If I implement it immediately on the "onsubmit" button, what happens if Aweber prompts user for a verification/bot detection etc, won't it screw up all the statistics?
Anyone guys? 
If i remember i think in Aweber there is an option to add subscriber in background via api, which means you make in funnel part "Capture email" own form, which has submit, than when
user click submit you process that in background and send user to Aff link, on sucess.
https://labs.aweber.com/snippets/subscribers
About tracking link it depends on what platform you use tracking so you need to see how it pass tracking. In this case funneling looks like
1000 on lander -> 200 submited email -> 2 converted on aff link
I think via visitId would be simple to track all this, so you pass visitId (clickID) from lander to capture email, than on capture email provide this to aff link (usually in aff_sub or subid param)