You CAN'T use both 44pin and 40pin header for primary channel.
You can. It's right that the 44pin and the first 40pin header share the first channel. But the adapter is designed so that you should be able to connect the master to the 44pin and the slave to the 40pin connector. The only thing you may not do is to connect master/slave to each header (i.e. three or four devices on the primary channel).