Add the NodeMCU ESP32 to your schematic (for example, assign it the designator U1).
Create net connections for each of its exposed pins to the corresponding PCB header pads using the default order. Based on the pads currently in your project, the mapping will be as follows:
With this mapping confirmed, the next step is to add the NodeMCU ESP32 to the schematic and then create schematic nets connecting each NodeMCU pin to its respective header pad as shown.