Where to Edit Phone Registry Hives?

Where can we go to edit the registry when we are building a Custom ROM?

I heard there were registry hives or something but I forgot the file names.
I see lots of tutorials for chefs and fixes to problems saying what registry entries to make, but I dont know where to put them!

Note: I am talking about editing ROM Build registry files from the computer, not from the actual phone.

Thanks!

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