General Hacking and Debugging of vB

I have just upgraded NoBlood.org to vB 3.6.3. I rely heavily on phpEd from NuSphere for editing and debugging. In my initial efforts to install vBSEO, when installing ioncube on my local test server (since my live server uses the same), I discover I cannot run with debugger module.

What options are there if any to inable php debug module with ioncube installed. Or if I have vBSEO installed, is it a matter to disabling vBSEO, switching back on debug module and turning off ioncube to do some debuging of vB?

Thanks for any observations.

(Just to clarify, it's vBulletin 3.6.0 Beta 3, not 3.6.3. )