To minimize (but not entirely eliminate) false alarms, you should have a single file to track banner clicks (which it sounds like you already do). Then disallow this file in your robots.txt as follows:
Disallow: /click.php
This will prevent the good robots (Googlebot, Yahoo Slurp, etc.) from tripping the alarm.
Next, you should set up a trap to catch and ban the bad robots. There are lots of articles on the net about this; see this page for an example. I would caution you to not use an obvious name such as “/bot-trap/” since this method has been around long enough I think most bot programmers would be smart enough to prevent their bots from going into something with the words “bot” and/or “trap” in its name. Instead, use a name which sounds like it would be a legitimate link.
Lastly, patience is the most important component. There’s no simple formula for determing what your conversion rate will be because there are so many factors involved, but I wouldn’t expect it to reach or exceed 1% for several months.
Profitable affiliates can probably chime in with more helpful stats about conversion rates than I can.