Can someone explain this to me?

Well there are two ways you can go about doing this. In either case one person has to act as the commissioner and then can control a team while the other person just controls a team. So you create a multiplayer league with a player for each of you and assign that player to the team you want.

From then you will have to decide if you (assuming it is you acting as the commissioner) wants to run things via email or via FTP. If you have a web server you can login to your league as the commissioner and enter the details for FTP settings in the commissioner office. You will also find helpful instructions there in setting this all up. Otherwise you can collect files via email from your friend. If you do this you will have to download his files, place them in the app/disk/Multiplayer/yourleaguename folder before using the commissioner office to import them. If you use the FTP method you can just click download files from the commissioner office and it will download them off the server for you.

The basic flow of things is
a) you provide the league files to your friend and he downloads them
b) you login as your player and make your changes locally
c) your friend makes his changes and exports a file from the office screen and either emails it to you or it uploads via FTP
d) you login as commissioner and import his file(s)
e) you progress the league as commissioner
d) you save and then provide the updated files back either via email or by uploading to the server and repeat the process

I recommend a quick trial league where you guys practice the flow of things so that you get them down before starting the real one.