To configure the remote and extender for Stand Alone Mode make sure that you choose the option
"Enable Wireless on Pronto Control Panel with Wireless Extender(s) in Stand Alone Mode" via the "System Properties\Wireless Settings" tab in your configuration file. On the extender end make sure that the
"Config" switch on the back of the unit is set to
"1 (Use)" and the switch next to that is set to
"Stand Alone". The Channel ID set in the software and on the back of the Extender also need to be the same which should be unless you messed with the settings. Under the "System Properties\Extenders" tab make sure to also add the Extender. You'll then need to go to the "Device Properties\Settings" tab for each device in your configuration file which contains actual IR code buttons (not links to IR code buttons in a different device) checking the Extender in the list which you added previously via the "System Properties\Extenders" tab. Additionally, as a starting point you should make sure that both the remote and extender are running with the latest firmware which can be downloaded here at Remote Central from the files section. To connect to the Extender via your PC to update the firmware see
here. Forget about the Extender Discovery Tool. I've never gotten it to work myself. There is an easier way. Just hit up the link and follow the steps I've outlined there.