I personally don't know the pin configuration for the firewire headers; having said that:
I was actually looking at getting a similar case/mobo combo to you (armor, p5w dh deluxe) and while reading up found that:
1)Thermaltake's manuals can be very hard to understand and contain A LOT of errors. I had a look at their PDF manual online but it doesn't seem that bad. Updated? Maybe the batch of stock in warehouses still contain an older revision?
2)The labeling on the Asus mobo and the manual don't match up. I'd go with the labels on the mobo
Top panel audio connectors-
ear - headphones/speaker
If its a little square shaped button near the bottom on the case, it should be the intrusion switch.
I am wondering which side of fan should put PSU in case? I am going to use hdd there.
I'm not sure quite what you meant but i assume you mean the orientation. On the armor case, the PSU can only go sideways at the the top. Remove the top HDD cage unless your actually using it as it blocks airflow. Having said that, if you don't mind whipping out a dremel, you could mod it yourself. Drill the holes to mount the PSU, then using a hole saw cut out a 14cm hole at the side of the case and fit a grill.
Check your motherboard manuel for proper orentatioon of the firewire and audio plugs. There should be a picture of it so you can orent the cable correctly. If not the black wires on the cable are the ground wires.
I looked at mobo manual it doesn't help much in installing IEEE1394.
I am confuse about audio plugs to. In manual it says about connector on mobo supports HD Audio and AC'97 Audio either. I know where is it. But the case's audio cable splits into 2 connectors: 1 marked as AZALIA, 1 marked as AC'97. Between AZALIA and AC'97 which connector shoud I use?