Here is what I have done for flats for years with good results, others may have different approaches:
1. I put a white T-Shirt over the end of my scope and smooth out any wrinkles so it is firm and flat (may need to be tied to the scope or a rubber band or something).
2. At dawn or dusk (usually dusk) I point the scope towards the west area and arund 15-20 degrees up into clear sky.
3. I take a flat using CCDsoft software. I take 3 flats for each filter. I aim for 1/3rd total exposure. For a 16 bit camera that is a figure around the 20,000 ADU mark. As dusk proceeds you will see that number drop from flat to flat so you have to move fast and you may need to increasr the exposure time as you go along to compensate for approaching darkness. I get them all done in about 4 or 5 minutes and this is where fast download speeds of the FLI cameras helps.
4. Because my FLI camera uses a physical shutter I find exposure times have to be about 3 seconds minimum otherwise you can see the shutter in the flats. SBIG cameras don't have this problem with their blade shaped shutters which don't have that effect. I believe you can also take flats with FLI cameras with some chips using video mode but that is not accessible to me in CCDsoft and I believe you need to use Maxim to get that feature.
5. I also take a bias, usually this is one from my library. Some say it is not needed, I take Stan Moores advice on this (the writer of CCDstack). I think it is a minor point and doesn't make a big difference but there was a reason which I don't recall clearly now. I think it was do with scaling images.
6. I combine the 3 flats I take, subtract the bias and use median combine or average to make a master flat.
That works fine. You do need to make sure the flat is taken with the same optical setup. If you change anything with your optical setup the flat is invalid. For example if you rotate the camera to frame a shot some dust donuts that were on the scope will no longer line up.
I take flats for each filter and they do vary in appearance from filter to filter so you can't just take one and use it on all of them. You also need to do your flats at the same binning you imaged at.
I hope the above helps. It is simple and easy to use but you have to remember to be setup and ready just before dusk. You can easily miss this short period of time when the flats have to be taken.
Thanks for the info Greg. When you say you aim for 1/3 of the total exposure (20,000 ADU) how is this figure measured? Is it an average or peak value? Does CCDsoft report this figure or are you looking at the histogram?
Thanks Troy. Geoff, the bias made a lot of difference to the flats processing as I was getting a light ring around the images without the bias. I've done the colour balancing manually.