I will have to go visual on how this works. In MakePE\Optional\ExtraFiles you will have several directories. This is how you inject Extra Files into WinPE.
In my example below I am adding files to WinPE 10 x64. I want to add msinfo32.exe as well as some OSK support. These files need to go in WinPE in Windows\System32. So I create out the directory structure in MakePE at MakePE\Optional\ExtraFiles\WinPE 5 x64\Windows\System32 and just copy the files in there. MakePE will handle the rest.
So why are there tons of other folders in there? Simple, for multiple combinations. For example let’s say I need a file in Windows on WinPE 5 x86 and x64. I will add the files to MakePE\Optional\ExtraFiles\WinPE 5\Windows
If I want to include something in every version of WinPE, then it needs to go into MakePE\Optional\ExtraFiles\All