You should finally have a good WinPE up to now, and are ready to add Drivers. MakePE uses a flat directory for installing Drivers, and these should be created automatically for you.
If you look in MakePE\Optional\Drivers, you should see these directories.
Simply place your extracted Drivers in the appropriate WinPE. In the example below, the Surface Gigabit Ethernet Adapter Drivers were added to WinPE 5 x64\Microsoft. No worries about subdirectories, they are handled automatically. Additionally in this example, I extracted the drivers from the Dell WinPE 10 Driver Pack. Now the next time I run one of my Build Scripts, my Drivers will be added to WinPE
The additional benefit is that I can take these directories and import the complete WinPE Version Architecture directory into SCCM, allowing me to keep the same source for WinPE, WinRE, MDT, and SCCM.