Install Question

I am about to install on a VB 3.5 board. The instructions say to upload the entire "upload" file. My question, am I leaving this in its own "upload" file with the board, or I assume not, I am uploading the files with the folder, into the root directory. My real question is, the upload file has image, includes and modcp folder, if I do that am I going to write over the VB files within those directories?

Your vBulletin files will be unchanged, the vBSEO files will be just added to corresponding folders at your host.