Simple.
Folder 1 should be named:
PS3
Folder 2 which you have to put inside folder 1 should be named:
UPDATE
Then the pup file which has to be placed inside of folder 2 should be named:
PS3UPDAT.PUP
I don't exactly know which version of Rebug your going too but maybe this thread could be of somewhat help to you?
Have a look -
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