it doesn't matter that there isn't a usb/other in your phones FS, no wrong the phone will place the file in the other folder in your phone, so when you turn the phone on the file will be there in the other folder, just plug the phone into the computer select usb transfer mode go to the other folder then copy the file to your pc then you can edit it.

After I edit the customize.xml file can I just replace the one thats in the custom dir with my edited one?

yes