If you open up the Quake folder, you should see an ID1 folder. Put your PAK files in there.
The structure should look like this:
ROOT:\Quake\
ROOT:\nxMakaqu.bin
ROOT:\nxMakaqu_scrambled.bin
By the way, it's not a selfboot, so you'll need to run it through BootDreams to make it selfboot.
As for TAoV, I can't help you, sorry.
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