The Assign Controller Functions dialog shows two lists. On the left received MIDI message appear when you operate your controller. The most recent message is automatically selected. On the right you see the possible functions for the selected message. If the selected message already has a function, that function will automatically be selected in the right pane.
When the selected message is a button the function list on the right shows functions that can be tied to buttons. These are functions that are like commands. The function triggers an action. Either directly in Premiere Pro, like start playback. Or they trigger a command for the PrControl plug-in, like "Select Layer 1".
When the selected message is from a slider or encoder, a control that sends a value, the right list will show functions that take value. These are functions that change some kind of level, like audio volume, or saturation.
Start with operating the control you would like to change, it will appear in the left panel. Then select the function to assign to it in the right panel. To find a particular function, use the search-box at the top.
If you want to have certain functions the same in another layer, you can use the copy button to copy from one layer to another.
If you are using a controller unknown to PrControl, PrControl has to detect the different kinds of MIDI messages the controller is sending. In case this does not work, you can override the detected type using the Message Options button. This button is not visible when you are using a recommended controller.
You can view the functions of each control using the extension panel. If you keep the extension panel open while assigning functions, you can keep track of what you are doing. And you can see which controls are still unused. Open the extension panel from the Window->Extensions menu in Premiere Pro.