Is it possible to force a fixed Application to open in a Secondary Monitor?

This is my first time actively using a forum, so forgive me if I'm unclear with my question or if I'm unaware of forum common sense or etiquette.
I've been running a Multi-Monitor system for awhile now at my office. I ran into a few problems when I first set it up, but was able to resolve many issues with many work-arounds. In truth, this is one of the same major problems I was having before.
As it says in my details, I have an iMac with a Wacom Cintiq 21UX via Mini DisplayPort to DVI, and an Apple Cinema Display via Arkview USB Display Adapter. I do a lot of graphical work amongst my many tasks, so the Cintiq is typically my main input device. I have it set in a Portrait position, which I prefer greatly over Landscape.
My problem is that to use many of the graphical applications, Adobe anything, I have to set it as the main monitor. Since Apple doesn't use application containers, at least, not in a way that allows you to drag the main toolbar. This solution, of course, I learned after a lot of struggle. It works and I'm fine with it now, but I've recently been called upon to use Final Cut and Motion for some projects and this problem has again reared its head, but in a different way.
I've programs set up all over my three screens; sized and set to where I like them and are most efficient, and across multiple Spaces. To properly run Final Cut, a resolution of 1280x800 is strongly recommended. Since I'm running Portrait, mine is set to 1200x1600. I didn't think much of Final Cut's initial warning at the time, since any windows caught outside the screen I was certain I could rescue with a trusty Applescript, written to collect all windows to the main screen. Which I discovered was a problem when running Final Cut from a laptop that was dual-monitored, but once you take away the secondary monitor the Final Cut windows remain floating aimlessly out of screen. They were floating off-screen, as I thought, and fixed it with the applescript. While I was working though, I was confused on where the **** the splice tool went. I looked everywhere in the application I could to find it, but it wasn't until I called a friend and he assured me that the tool actually did exist that I remember the teeny-tiny tool panel that would typically reside next to the timeline. The applescript can't pull it for some reason.
So my question, *is there a way in which you can change the display an application starts in?* (bolded for ease of discovery in this long post) what would fixedly open in the main display instead opening to a secondary monitor. Or, as consolation, possibly rescuing that tiny tool panel? Early on I tried keeping a shortcut key set to switch the main monitors back and forth, but found that applications will switch with them, applications I didn't want to switch. Plus, the Wacom Pen has to be re-calibrated when the Cintiq is switched to the secondary monitor, and then, of course, re-calibrated again when it's switched back to the main.
Any help would be greatly appreciated. Thank you.

All my Monitors are set to their native resolutions, 1280x800 is Final Cut's suggested optimal resolution. My Cintiq is a Tablet Monitor, one that allows you to write or draw upon the screen itself, as such, it's set upon an adjustable stand that will let you place the Tablet Monitor upright, semi-flat against the desk, or anywhere in-between, in addition to 360 degree rotation in its flat position. This means that the Tablet Monitor comes with two native resolutions, one for Landscape and one for Portrait. The Cintiq is purposely designed to allow it to be set in a Portrait position, for the comfort of the User. 1200x1600 is just as native for the Cintiq as 1600x1200. Also, my Office Desktop set-up is, God-willing, a permanent set-up; I don't disconnect Monitors, and they are set to Extended Desktop Mode.
My aim was to avoid switching back or forth between resolutions or Mirroring. This will work, yes, but having to do it every time I need to use Final Cut, or any other such program with odd monitor requirements, is a hassle. With all the various windows and applications I have running at any one time, I'll be wasting time moving and resizing windows across multiple Spaces back to where they were every time I need to run Final Cut, and re-calibrating the pen to the new resolution. Which is also a little embarrassing when I need to demo a clip for my bosses and co-workers and I have to spend time, in which I could be explaining things, tiding up my desktops. It would be ideal to have it prepared before they got there, (actually, ideal would be not having to prep it in the first place) but not all meetings are scheduled and planned.
As for windows that get lost in space, that's what the Applescript was for, but apparently that little tool panel, which is wholly more important than it's size suggests, doesn't register as a window and gets left behind.
So my hoped for solution is a way in which to force a Program that would normally load onto the Main Monitor to instead load on to a chosen Secondary Monitor, one that fills the necessary resolution requirements of said Program. I couldn't care less about the Applications need for the Main Toolbar since I run Secondbar anyhow.
This isn't a vital emergency though, I'm just trying to find a solution for an annoyance and to make the whole process more efficient. Oh well, C'est la vie.
Thank you for your reply Dennis.
Message was edited by: TimR.NSC

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