How do I treat the WooCommerce Ajax Endpoints

I had to switch on Ignore URL arguments for my installation, because I had problems with my Affiliate plugins that added parameters to my pages. Now I am trying to do some filters for the WooCommerce Ajax endpoints that come in the form of: yourdomain.com/?wc_ajax* and yourdomain.com/?wc-api*
How can I make them work? If the frontend does not allow that because of my settings, is there a way to do that programmatically?