Well, let's see....
1. If you go from the two connections on the amp to two connections on the bass and two connections on the treble, then you are bi-wiring. In this case, remove any jumpers or connections between the bass and treble binding posts.
2. Shot gunning means you run 2 cables between amp and speaker. There are two connection possibilities: A) Tie both reds together, then tie both blacks together at both sides, or B) tie both leads of a given bundle together (red and black) and use as one channel, repeating with the other cable. Both of these double the conductor mass per channel.
3. This depends on the type of connector you have on the amp. If you have binding posts and the cables have spade lugs, just use two spade lugs per post. If you have bananas or pins on the cables, well then you have to play around a little. You may have to reterminate the wires. If your amp doesn't use binding posts you may need to make an adaptor.