I am making sure that my image train is the same every time that I start an imaging session. If I take UHC Flats and Dark Flats I follow this with UHC Lights and Darks.
Thank you for your description on how you take Sky Flats. This certainly is a viable and simple option. Personally I chose getting a light box as I was aiming for longer flat exposures which I have heard from some that this camera prefers. At the time I tried Sky Flats I had a 10 second download delay (now this is 2 seconds with PowerLine adapter) with Ekos between 5 second Sky Flats. By the time the images were completed the ADU variance due to the darkening sky was over 10,000. Of course a light box carry's it's own set of challenges, such as adding on T-shirts to deaden the light over longer exposures.
The main thing is to stick with what works for you.