In PEP2/3, you need to click on each piece of equipment and select whether or not it is using the extender in question and which IR port should be used for the equipment. Under Building Blocks -> Equipment & Codes tab, when you click on a component, on the right-hand side, you will see 'Select Extender' If an extender is being used for this component, the box to the left of your Extender will be checked and then you must select the IR Port you want to use via the drop-down.
Under System Properties - Network tab, you will want to select the radio button 'Use Control Panel' - 'With Wireless Extender(s) in stand alone mode. All your extenders must be set to run on the same 'Pronto Channel' and each one must have a unique Extender ID.
When using Standalone, the Extender and the Pronto operate on an ad-hoc wifi network named ProntoNetwork1, ProntoNetwork2, ProntoNetwork3 depending on the channel you select on the RFX extender and on the pronto.
If you are going to use Standalone mode, your Pronto does not connect to your router and you will not be able to access anything via the web or other equipment on your network.