take a look at the info in this thread:
PowerShell script to create symbolically linked (mklink) copies of WoW

not only will this allow you to have separate settings for each of your toons, it improves performance/load times considerably

also, here's a thread with info on backing up macros locally:
Macros now serverside

To backup your macros, log in and set up your desired variables. Then, into the chat window type:
/script BackupMacros()

This will cause your macro list to be saved locally within your **WTF\Account\<Account Name>\<Realm Name>\<Character Name> folder as "macros-cache.txt".


Once saved, you can then upload these settings from your local file to our server by using the following command (again, while logged in and typed into the chat window):
/script RestoreMacros()