I don't know if I'm totally following this but I thought I would give it a shot with what I thought you're looking to do.

First off, nofollow is good to do on your affiliate links. But I would suggest a JavaScript link through to be absolutely sure that the affiliate link does not get any credit for being a link.

Now what it sounds like you are having a problem with is that the url you type in on your website/blog is being altered after you insert it. One solution to this which would also give you a nice URL for your visitors would be to use a url re-write mod (.htaccess) and redirect users to the affiliate page from one of your own pages.

Such as:
Affiliate page: http://www.affiliatecompany.com/category/product/mycode
Your page that redirects to affiliate: http://www.yoursite.com/affiliate/product

Now in your htaccess you would send all pages ^/affiliate/(*+)$ to a PHP page (maybe /affiliateredirect.php?product=$1) that would redirect the visitor to the correct affiliate page based off the product.

__________________
Providing SEO services and business website design.