So is your question how to add auto-assist + broadcast keys to the 1 through = that are there by default?

What it boils down to is "I want to press ____, and have it press ____ in the other window". You can do that as many times for as many different keys as you want, with or without the auto-assist. You can copy existing mapped keys in the "FTL DPS Keys" map like so:
1. In the top pane under Key Maps, select "FTL DPS Keys"
2. In the bottom left pane, right click "DPS 1" and select "Make Copy"
3. Rename the copy
4. Click the < button by the Hotkey on the right. This is how you activate the mapping, and it doesn't have to be similar in any way to what it sends to the other window.
5. Expand your new hotkey in the bottom left so you can see Steps, 1 under it, then click on 1
6. On the right you'll see 2 Actions in the Step. The top one handles the auto-assist, leave that alone unless you want to remove auto-assist from this key (in which case just delete it). The bottom one says "1 -> all", select that and change the Key Combination to what you want it to press after assisting. If you only want specific windows to press this key, change the Target, otherwise all windows will do it.

That's it, you can File, Export and ISBoxer will reload this and let you use the new mapping in game immediately.