The pin out is different for the 6FQ7. Although it is a good replacement, (6SN7 in 9 pin small bottle), you will need to make some simple changes to the heater wires. The 12AU7 uses a 9A Base and the 6CG7/6FQ7 uses a 9AJ Base. The only difference is the connection of the filament voltage.
In the 9A, (12AU7), base one leg of the heater voltage is connected to the number 4 and 5 pins and the other leg is connected to the number 9 pin. To convert to the 9AJ base, (6FQ7), simply move the 4 and 5 leg to the number 4 pin and move the number nine leg to the number 5 pin.
From your post, I am assuming that you didn't build the Crack. If you are not comfortable around tubes, high voltages and soldering, I suggest putting the 12AU7 back in and enjoying the Crack for awhile. Then, if you want to do some mods, after you are comfortable, it is a pretty easy, and reversible process.
Cheers,
Geary