Frankly, I don't know because I haven't done what you are describing. But, I would say that resolution is the *entire* issue. If you've got the same resolution running on your 4:3 and your 16:9 monitor, one of them is going to look out-of-whack. The widescreen will either look stretched, or the traditional will look skinny, depending on the resolution.
It's funny to me, because widescreen displays for PCs and laptops are all the rage, and what you are really getting in those is NOT a wider screen, but a shorter one! The resolution, instead of being higher, is usually lower. Resolution on my LCD monitor on my desktop (not widescreen) is 1280x1024. For the widescreen on my laptop it is 1280x768. Widescreen? Try "chopped-screen".
If you are outputting different resolutions on your 2 monitors that are running from the same video card, then sorry but I can't help, because I just don't know how that works...