Put cookie on main entrance page?

Hi,

I've implemented an affiliate scheme and I wonder where
the best place is to land the visitor who comes to the web
page from a banner?

I put a cookie on the landing page so I can track the visitor
to see if he/she purchases a product.

Is it safe to put a cookie (with a Javascript) on the ordinary main page?

Will search engines protest? Are there any other problems, besides
that the user might have Javascript switched off, but that's not a major
problem (I assume).

Or should I land the visitors on a different page? However, I don't want
to create a special page for the visitors who arrive from a banner. I don't
have any particular ideas concerning what such a page would contain.
I'd prefer the main page.

Regards
Mike