Well, the way I do it now is to delete all the products that was not cross sell correctly then hit cleanup XSell to delete relations. To add more cross sell to one product that already has cross sell, I just add new cross sell list of the item, the old cross sell item and new cross sell item since the module is smart enough not to add duplicate.
I haven't tried putting cross sell on the checkout page. But, can't you just copy the code that is suppose to go to the product page to the shopping cart page?
Thanks
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