I literally just had a post like this the other day. I went here to figure it out.... http://openiv.com/?p=1132

Whatever file you're replacing or doing anything with, right click on the main directory and there's an option, "copy to mods folder." That entire directory will be copied into "mods" and just go from there. You only need to copy a few directories...

x64e (rage package file) Contains all main GTA vehicles
x64i (rage package file) Contains vehicle body mods
x64w (rage package file) This is the SPupgrade with the dukes o death, marshal, seaplane etc.
update (folder)
common.rpf (rage package file)