Hi Paul, I hope this will help you:
1) You cannot use different filter setting for taking lights and flats. This will result in a different "light profile", for example the UHC filter will cut some part of the light spectrum and resulting flat cannot be used for calibration of lights, that are taken without such filter.
2) Taking sky flats in Ekos is really easy. You just sset target ADU with some +- variance and the software will do all work automatically. You just need to take exposures during dawn or dusk, on the opposite site where is sun. And the sky needs to be clear, without clouds. You can start with exposures 10 - 20 minutes after sun is under horizont. If exposures are short, you will skip and wait few more minutes and repeat this steps until you get exposures in range you want, e.g.: 1-3 seconds. Once ADU are not in the specified range, ekos will automatically calculate new exposure time. And this will repeat until you get enough exposures. I am taking 12-20 exposures. 
I hope I wrote it understandable

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