Upgrading - Confused

[JLS]

I'm upgrading our test forum to 4 so that I can create a new skin. Once I have that I'll upgrade our live forum. 

But.

One thing that I'm confused by is it says to download the IPS folder from my client area (done). Then upload the contents of that folder to the root forum folder via ftp and overwrite when prompted. Are they saying I should overwrite my "uploads" folder with theirs? I believe that would delete all our forums images? But if they are saying to "drill down" into the deepest depths of the folders and overwrite any updated files or add any new ones that would take hours or days with the other folders...LOL. I've also come across things saying not to overwrite my config_global or config_global_dist (can't remember which it said or both). 

It's very possible I'm being an idiot over this but can someone explain if I'm supposed to not overwrite certain folders, drill down deep into the folders, or just overwrite everything with fingers crossed including the uploads folder like the instructions seem like they are saying.

Thanks

[JLS]

*bump*

[JLS]

I think I've figured it out. I was never aware that there was a "synchronize" feature of the FTP program that just replaces old files with new ones. I'm sure that must be what was supposed to happen so I proceeded with that and fingers crossed I was correct