Yes, I use darks when using the internal guider. Maybe I eliminate the gain setting. I've purchased a new guide camera (ASI290) to replace my ASI120. I'm beginning to suspect that the camera is part of the problem.
I've always used PHD2 until a couple of weeks ago. I suspected that I was having communication problems between PHD2 and EKOS, which was causing some guiding problems. Since moving to the internal guider, my results are much better.