The AirPort Extreme only has 3 Ethernet ;ports, so unless we are not understanding your information, or you have additional equipment that you have not mentioned, I'm not sure how you are able to connect more than 3 AirPort Express devices to the AirPort Extreme.
Can you provide more details about that?
In any case, when configuring multiple AirPorts, you would configure one at a time. In other words, only the AirPort Extreme and one AirPort Express should be powered up at any given time until all the AirPort Express devices have been setup.
Should I disable wifi on some units as I configure them?
Sorry, I am confused by your question. You should be using the setup "wizard" in AirPort Utility to configure the Express devices. The setup "wizard" will not have an option to disable wireless during the setup process.
As far as the number of AirPorts that could be connected to an AirPort Extreme......assuming that you have a number of Ethernet switches, the theoretical limit would be about 250 Express devices.