Does not really matter what my guess would be as I have tried it both ways. Second way does at least tell me the files failed to patch tho, lol.
I gave the paths where the files need to go... put them there and run metainjector. Choose "keep files" like the program tells you to because the "let the program decide" option no longer works, like the red warnings tell you when you run metainjector after resorepless...
Everything in .resorepless folder gets deleted everytime you run resorepless like the program tells you when you run it (the program is quite well written and gives a lot of infos and warning for those who read them), that's why your files disappear.
Everything in the NOT .resorepless folders will overwrite files with same names in folders with the same names that are in .resorepless. That's the folder structure of the game you want to keep so the new paz can overwrites correctly the vanilla files.
If they failed to patch, make sure the files are in the right place and with the right names.
For instance, you want your _nude_ files to be in the nude folder and not sho for instance. The "failed to patch" messages will list you the whole thing so you can easily check if the files are where they should be. pac go in the "model" folder and .dds in the "texture" folder.
Otherwise, as you're autopathing or cooking/chopping in game, I advise you to read these forums starting on page 1. They have a lot of infos, take a while to read, but what else are you gonna do while you wait for your dishes to finish cooking ? :P