---making a big mess of files and folders.
Yeah that's usually the problem with multiple workflows. Some things to consider:
How do you want to catalog your images and what program do you want to use for that purpose? Explorer, Dropbox, Bridge, Lightroom, Capture One? Since you shoot to print, I would think one of the last three might have an advantage.
How do you want to utilize Capture One? All image development or a few select images that you can't seem to get the way you want through ACR? Or something in between? That's a big factor, and something that may be tough to answer initially.
Do you have a preferred print path? If you always plan to print through CS5, then it seems to me Bridge should be your "control room", exporting tiffs through Capture One when necessary.
Those are the initial questions I suggest you think about, then structure the filing workflow to fit your preferred path.
Dave