Finally, I was able to have two separate accounts launch for me. I found that the Launcher.exe file wasn't closing when it should have, so I have to manually force it closed by ending its processes in the task manager after the 1st one logs in.
If the issue was the first launcher still being open, sounds like you were getting an error message indicating "Only one instance of this application can run". Knowing that would have helped me help you sooner.
I ended up with a stretched out window layout
If you didn't disable Instant Swapping for your Window Layout, either during the Quick Setup Wizard or after, then your windows may look and operate wrong. This is one of the main two points made in the
SWTOR howto 
You can disable it now -- in the top pane in ISBoxer select your Window Layout, then in the bottom right pane uncheck the "Use Instant window swapping" box, then Export.
I'm pretty sure my pc can handle it? But for some reason it performs like ass >.>
Alienware Aurora- Windows 7 Ultimate 64.
i7 20 @ 2.67 2.67 Ghz core
Duel ATI Radeon HD 5670 video cards
I take it your 2 video cards are in Crossfire mode? Crossfire (and SLI) support in windowed mode is hit-or-miss, I would grab GPU-z or maybe MSI Afterburner or something and see if your second GPU is idle. Ideally when multiboxing you would have the two cards powering two monitors, and then with 2 characters you'd have one GPU per character and they have their own screen. More on this topic:
GPU ManagementI can live with this for now, but I'm not sure how to set it up like LAX has on the main SWTOR post having the one full screen and the other window in the bottom corner
Right above the picture it says "But here it is working correctly on one PC, using
Video FX to see and interact with the other window, instead of a Window Layout". With the link! Click the link, and there's a ton of information including pictures and two different videos that demonstrate how you can do exactly what you just asked.
I am having some in game control issues with both set of characters not staying together as a group. When running they seem to drift apart. I'm sure that some hot-key that I have yet to learn will fix this.
First,
FAQ: Why do my toons move in different directions?Second, one of the problems people are having with multiboxing in SWTOR at the moment is that the auto-follow functionality in the game is almost completely useless because it is currently broken. There's
a thread about it here and
one on dual-boxing.com. Hopefully Bioware takes care of this problem not only for us as multiboxers, but also as people who have to get up to pee once in a while as we play their multiplayer game. So far we don't have an official response about it other than a customer service rep suggesting that the right way to get this fixed is to use the bug report system in the game (type /bug) to report the problems with auto-follow. The more of us that report the problem, the sooner it gets solved
Until then, people either are doing what you are doing and putting up with drifting apart and having to manually adjust a lot while moving, or putting up with auto-follow breaking after a few short seconds on the chance that it DOES work.
Fri Dec 23, 2011 9:09 pm 
