It's really easy actually.
Make a file called "COINNAME.conf" in the directory where the coin data is stored, and put the following in there:
listen=1
maxconnections=100
gen=0
genproclimit=-1
rpcuser=USERNAME
rpcpassword=PASS
rpcport=9031
p2pport=9031
rpcallowip=127.0.0.1
server=1
daemon=1
You need to put a username and pass there, anything is ok.
Then make a shortcut to the coinqt.exe, go to properties of the shortcut, and add "-server" behind "target".
Then setup cgminer to mine at url
http://127.0.0.1:9031, with the chosen username and password.