Both Zend and Ioncube will work on same server.

You need to add Ioncube first, then Zend, some thing like

Code:
[Zend]
zend_extension = /usr/local/lib/php/extensions/ioncube_loader_lin_5.2.so
zend_extension_manager.optimizer=/usr/local/Zend/lib/Optimizer-3.2.6
zend_extension_manager.optimizer_ts=/usr/local/Zend/lib/Optimizer_TS-3.2.6
zend_optimizer.version=3.2.6

zend_extension=/usr/local/Zend/lib/ZendExtensionManager.so
zend_extension_ts=/usr/local/Zend/lib/ZendExtensionManager_TS.so