Tips to negate chaos long-range:
#1. With AAF you can close from >60cm to <30cm in one turn of movement, and be certain of hitting with every torpedo. You should manoeuvre to just outside 60cm to set this up. To stop you getting the first shot off, he will be forced to close with you. So you're looking at a max of one turn of unopposed fire.
#2. Screen his shots. Have a squadron of cruisers lead the way, and try and make it so that some of his ships will be closer to one than the other. He'll be forced to target both of them, which will waste firepower against shields, and he'll be very unlikely to cripple them. If he wants to shoot anything else, that's a leadership check, and assuming a ld of 8 he'll fail just under 30%, taking the heat off your more valuable ships.
#3. Wasting firepower on your battleship is good. To cripple a healthy Emperor before you get into torpedo range will take an average of 32 long range lances, assuming 30% of shots are unintentionally directed at other vessels and the Emperor braces after losing its shields. Even Chaos doesn't have anything like that kind of one-turn firepower, and certainly not at long range. Put it close behind the screening cruisers to positively encourage him to shoot it.
If you follow the above tips, the majority of his firepower will bounce off your most heavily protected vessel, and what's left will dissipate harmlessly off the shields of your screening cruisers. In the following turn your Emperor can take up a more defensive posture, and your main line will be in position to gut the centre of his fleet. Now enjoy watching the heretics burn.