I can help answer #1:

It's going to depend on your play style and how you choose to set up your macros.

The way I do it is, I have 1 main key that tells the slaves to assist my main. There are no other /assist commands in any of my keys.
This works well for me while tanking as I can change targets to gain/gather aggro, and let my slaves continue to DPS the original target.

I haven't run into any major problems with this setup...they simply don't cast if they don't have a target.
And, since I'm not using focus for anything, it frees that up so my main can pick a target to sheep/banish/shackle.
The slave can then /focus the mains current target and keep it under CC for the entire duration while continuing to DPS the main /assist target.

The FTL system is great and I highly recommend it, but I won't be much help setting it up with HotKeyNet.
That being said, there have been several others who have it working with HotKeyNet and I'm sure they'd be willing to give you a hand.