It seems like a pretty straightforward routine to take flats with Ekos. But being new to this there is always a niggling feeling that I might be doing it wrong or could be doing it better. Here is how I am taking my flats:

1. White t-shirt flat and stretched over end of OTA.
2. In Ekos I select "flat" and in customize I leave it at "manual". I leave ISO the same but on my 6D select AV (rather than BULB setting).
3. I start capturing while using my iPad on full brightness holding it pressed up against the white t-shirt.

My flats look good I think. On the histogram they are about half way exposed.

Am I doing the right thing for good flats?

Yep. The important thing about flats is to have the exposure in the linear range of the sensor, since the calibration math assumes that. If you want to go all OCD you can switch the orientation of your iPad between two images, stretch them, then use your processing software (e.g. Difference blend mode in Photoshop, I know there's a spell to do it in PixInsight too) to check for any inconsistencies in the screen illumination.

Of course, you can do that with just a couple pictures of the iPad, for that matter.