Answers to your questions:
"which wires do i join if i do join the wrong wire will it kill anything" - no that speaker will just be out of phase. Either look at the other wires to see if you can work out +ve and -ve, or use a THX optimiser to get this right by listening to the test tones.
"which output on the amp do i use" - The surround back speaker output.
Major consideration, as you will be connecting this speaker directly to the amp you should avoid sending the low frequencies to it (according to the Mission support guys). As the sub manages the crossovers for the other 5.1 parts (everything below 200Hz and LFE output via sub), you should:
- Set "Left", "Right", "Centre", "Surround Left", "Surround Right" speakers to LARGE
- Set "Surround back" to SMALL
- Set the crossover to 200Hz
Take it Easy