Hi,
There is a lot more involved in order to have two different checkouts. The checkout=1 parameter just tells the system to redirect to the checkout after the product is added to the cart. You would also have to modify the checkout controller and the checkout views in order to handle several checkouts. That would include a bunch of hacks.
The best would be to allow the checkout workflow to be overridden by hikashop plugins. That would enable you to do it more easily. But that's not yet possible.
If you want to activate the affiliates by default, it's quite easy. Just change the default value of the user_partner_activated column of the hikashop_user table to 1 via phpmyadmin and all the new users will be affiliates by default. You don't need that checkbox.
If you still want to use the checkbox, you should try to replace the line:
$affiliate = 'CHECKED';
to:
$affiliate = 'checked="checked"';
in the file components/com_hikashop/views/user/view.html.php that might help solve the problem.