You definitely don't want flats to be the same exposure time as the lights; you would end up with something completely saturated. As the Starizona article referenced above says, you want the average value in the center of your flat frame to be somewhere around 1/3 to 1/2 of the camera's saturation value. Personally I go for something near to 1/3.
Also be aware that, depending on your camera, if flat frames are very short, they can be compromised by effects from the shutter opening and closing. If your flat frames are at least a second, this shouldn't be a problem. This may, in turn, mean that you have to set the brightness of the flat box quite low in order to get an exposure time that's long enough without the level being too high.
The result should show up any vignetting in the optics, as well as any dust in the optical path. Dust motes will show up as donut shaped shadows on the flat frame, with a size and darkness that depends on how close to the optical sensor the dust is. You want to capture all of that because the flat calibration process will compensate for the effects of dust. For that reason, it's very important to not rotate the camera or filters between taking lights and taking the corresponding flats.
Once you have figured out an appropriate configuration of flat box brightness and exposure time, you want to take a sizeable set of flats. I take about 30 for each filter.
One more gotcha that I've run into sometimes: if the flat box uses incandescent bulbs, when they're turned down to get exposure time into a reasonable range, the spectrum shifts to the red end. What this means is that if you have incandescent bulbs rather than LEDs illuminating your flat box you need to check the levels independently for each color channel. I switched to LEDs a couple of years ago, but when I was using incandescent bulbs I would always have to turn up the brightness in order to take blue flats...
Anyway, hope that helps, and best of luck
Duncan
