1. What alcattle said. If you watch the 40 second configuration video long enough to get to where I'm logging into the game, this is specifically described in an annotation. Hit Shift+Alt+M once or twice to disable key maps (it'll say on the screen whether they are on or off) for login -- the auto-assist action bars is active at login so that is interfering, and disabling key maps will prevent that so you can type the numbers in your password.
2. WindowSnapper is the name of the script that runs the "PiP" functionality, although most people do not use it for actual PiP (which would be defined by having one window shown inside the other) because it would block some useful real estate on the main window. Like Svpernova09 said, you'll want to make a Window Layout just for the second PC (make sure to select the second PC from the drop-down that says "Pre-defined Computer" so the monitor layout matches the second PC instead of the first PC), and you will probably want to disable the Swap option (or set it to something other than Always, since disabling it may mess up the resolution for #3)
3. For mouse repeat to be accurate, they do indeed need to be in the same resolution. If they're not in the same resolution, you can't expect things to be in the same place on the different windows anyway. There's multiple ways to ensure they are the same resolution -- if they're on the same PC, leaving Swap enabled (but you can change it to something other than Always) is sufficient. Otherwise, you can always set the Desired Rendering Size to match on all.
4. Unfortunately the way the FTL generation currently works in ISBoxer, it is only generating the FTL for the individual Character Sets. However, you can manually set the FTL macros (the 3 in General key map are Follow, Assist, and Target) to include all of your characters. It will be slightly more difficult to switch between teams, so if you go this route you might benefit from keeping multiple ISBoxer profiles if you want multiple teams.
Here's what you do:
Make sure that the selected FTL Modifiers for the characters on the second PC are different than those on the main PC. These are selected per Slot in your Character Set. Go to the FTL Follow Key, in Step 1 where the actual follow action is defined, and select one of the two teams by hitting the * button next to the Target drop-down. You should see the "final macro text" change. Select the final macro text, and copy it to clipboard with the keyboard shortcut CTRL+C (right click won't give you a menu to select copy from in this case), and paste it into notepad or some other convenient text editor. Then select the other team the same way you selected the first. Then select just the FTL sequence from this team, and make sure it goes after the original sequence you pasted in notepad. Paste the completed FTL follow command into the Commands box, and make sure there are no "targeting options" selected
Repeat the same thing for the Assist and Target keys. Make sure there are no targeting options selected for any of them once you are done, so the final macro text shows exactly what you put in the Commands box.
Then everyone will be able to follow, target, or assist each other.
5. The performance hit you're talking about is most likely caused not by your video card itself, but by the way DirectX works. If you move a window from a display controlled by one video card, to a display controlled by another, it will be software rendered, resulting in a massive system slowdown. Rumor has it that if you use Windows 7, that you can do this without that performance hit (I have not tested this myself, but Zanthor reported good performance with a 3 monitor setup on Windows 7, and I heard a similar story from at least one other person). Anything prior to Windows 7 and you definitely get the performance hit.
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