One simpler method is to just have one pools file and use it for all your GPUs. You only need separate files if you actually want each GPU going to a different pool.
Feeling rather dense tonight. So if I create one pool file for 9 miners on Deepbit the three separate machines hosting the 9 GPUs will read the file (on each machine, haven't done a single config file yet) and they will all 9 find a miner account on Deepbit? I must be missing something.
you need one pools file per machine, though the managed config option can help you get a single central file onto all the machines. for instance I have one pools file running 12 machines with total of 30 GPUs. it is stored on a server, and all the rigs pull the file using rsync. this is through the managed_config_command in bamt.conf.
a simpler compromise would be to just copy the same pools file onto all your machines, if you don't change pools a lot that will work fine.