Contact ANet support, and explain your situation.
http://www.guildwars.com/support
Tell them you created a new account with Factions by mistake, but you intended to link it with your existing account. Ask them to link it for you.
Just so you are aware, you don't actually need to install any campaigns or expansions after the first. For example, in your case, after you install Prophecies, it's not necessary to install Factions from the disk. The only thing you need is the CD Key, and there is an option to add a CD Key to your account.
It's in the log-in screen, right below your password. This is what you will want to do if you choose to add Nightfall to your account in the future.
