1) If your head unit has front and rear pre-amp outs you can use the fade as you described. If it only has one pre-amp out you will have no fade.
2) I would run the sub controller if you have it, it is nice if you listen to a wide range of music genres. As well, if your head unit does have front and rear outs, then you can run the boat and sub off the same side and when you fade to the tower the sub will lessen with the boat speakers.
3) You will have 60 watts at each speaker.
4) Nice and load.
Problem you may run into is overheating of the amp because you are running everything at 2 ohms. It may cut out at high volumes but you won't know till you try. (It won't hurt the amp.)