I've now got online to work and I can still use patches/mods offline, using this method courtesy of Outsider87:
Yes you can have 2 different FIFA 09. I have them now! There are 2 way to do this. The most easy way is simple: just make a backup of FIFA 09\data folder, rename it "data_online". Then, when you want to install a patch install on FIFA 09\data and play normally. When you want to play online just rename data into data_offline and data_online into data. That's it. Another way is to duplicate the whole FIFA 09 (as I do from years) and then change the registry to switch between the 2 fifa. This thing is a bit more technical. I have a italian guide about it, if you want I can translate it in english However also the data backup works very good
This was the only way I could do it, means I have to rename a couple of things, but I don't mind.