Is there a way that I can set this up where no matter which window is active a certain key press will activate those keys on another window? Or at least set it up where 1 button will do it on the active screen?
You're looking for the Mapped Key Wizard. It's mostly painless. It almost doesn't require an explanation but here's what you do:
1. Under Wizards select Mapped Key Wizard
2. Select a Key Map to put the Hotkeys in; you may only have "Always On" if you have a default setup for EVE. The drawback of putting these under "Always On" is that you can't toggle the Hotkey off, so you might also consider creating a new Key Map for them first (right click Key Maps, select New Key Map, name it something, and then add it to your Character Set)
3. Select the type of Mapped Key to create. If you want to send the same key you press, select "Straight Key Broadcast"; if you want to send a different key than the one you press, select "Key Re-Map"
4. On the last page it lets you set up one or more keys (re-map will only do one at a time, straight key broadcast will do as many as you want). pick the key you press, the key to send, and where to send them to
5. Finish the wizard
6. Export to Inner Space
I also would like to know how to minimize the game clients, I can hit win+D and they minimize but the second I try to open something on the desktop they pop right back up.
You cannot
minimize the game clients if you have a Window Layout. They will do their best to stay in the defined Window Layout. You should be able to Win+D and *activate a non-game window*, and the game windows will not automatically pop back up. They will come back up if Windows automatically reactivates one of the game windows, which can happen if you have nothing else running already. I'm using Win+D just fine with my game windows all running and using a Window Layout like this.