I know exactly what you mean, and I'm doing it for my rig to.
This is how I did it.

Copy the directory of cgminer to a dedicated directory for every gpu you own.

Then do something like this for every gpu. Make a script for running your tasks
This one is for gpu0:
Change the bold/red to your needs

#!/bin/sh
cd /home/miners/cgminer-gpu0  #point to the directory of you dedicated instance of cgminer
rm *.bin
export DISPLAY=:0
export GPU_USE_SYNC_OBJECTS=1
./cgminer -d 0 -o stratum+tcp://mint.bitminter.com:3333 -u xxxx -p XXX -I 9 --gpu-engine 1160 --gpu-memdiff -150 --temp-target 60 --temp-overheat 70 --temp-hysteresis 3 --temp-cutoff 80 --auto-fan --gpu-fan 25-85 --vectors 1 --worksize 256 --failover-only --gpu-threads 2 --no-submit-stale --remove-disabled


Run the script.
Now you have a instance of cgminer for every gpu
This is a linux script but if your running windows you could make a .bat script.

I'm using bitminter pool for some time now, i'm very happy with it. I'm on the edge of switching to litecoin. The difficulty on BTC is getting to high, for my gpu mining rig. I was experimenting with litecoin for some days and exchanging them into BTC gave be a better profit then mining BTCc alone. But If I mine for LTC that would mean I have to leave the BitMinter pool. I don't want that.
Now here is the thing:
DrHaribo: Could you get support for LTC. That way I don't have to leave you. You don't have to build a client for it instantly. There are already LTC clients. Just setup a server alongside. I think this is the way to hold users on board, and keep this fantastic pool a life and growing. With the difficulty rising to the roof and other alternatives (LTC) its better to have an alternative aside. instead of seeing many gpu user jump over to the LTC pools and loose them forever! I think the main PRO of bitminter.com is  the friendliness of the users and operator(s). We could have that with LTC to.

This make no sense at al for a forum: It seems that I can do a search only once every 360 seconds. When I use the search bar twice in a certain timespan I get an error saying that my latest post was less that 360 seconds ago.
Am I missing something here?