as long as the folders are the same name, just put it on the memory stick as normal and it should copy over the old.
BTW, the new version of PBPmaker has an english exe so you can understand it all now. and it has an option to change the icon for when its on the PSP, i made a few of my own

plus it has a sort option, you can arange the order the icons will appear on the psp.
i deleted kxploit off my computer now. pbpmaker is so much nicer.