Nessa has a guide posted showing exactly how to get the IonCube encoder installed right alongside the Zend Optimizer (specifically on a cPanel setup).

This is a common request we get for Ioncube to be installed. It's generally not an issue, but when you factor in other optimization plugins like Zend and eAccelerator, a common misconception is that the three don't get along. It's very easy to install Ioncube into a PHP installation that already has Zend and eAccelerator.

It's only about a five or six step process to get them working happily together with one "gotcha" mentioned about the ordering of the statements in the php.ini file.