I've had the Eheim dual feeder for some years & yes, it's a bit of a conumdrum with respect to feed amounts between pellets, flakes & other types of food. I find it doesn't feed larger flakes very well and as you've experienced, tends to dump a good load of pellets per feeding if that's all that's in the hopper.
While the dual chamber design is a great idea & lends itself to using each chamber for a different type of food, I've found that it's best to mix flakes & pellets together in the same chamber. I used to use pellets in one chamber & flakes, dried shrimp in the other when I first got it, but had the same experience as you with too many pellets dropping per feeding. Now I fill each chamber with a spoonful of flakes first (poke the large ones down between the auger screws with a toothpick), then a few pellets, another layer of flakes & so on 'til it's about full. What ends up happing over the time period it takes to empty the chamber, is the pellets tend to migrate to the bottom of the chamber past the flakes & you'll still get a bunch of them hitting the water at that time. However, if you refill the chamber the same way before it gets too empty, this effect is minimized.
I've also made an HOS acrylic mount for my feeder which holds it on the side of the tank & at a slight tilt to help the 'large' flakes come out. The mount features a rectangular extension that goes below the water line allowing flakes & other food that may float into an overflow to soak & sink minimizing that issue. I've posted photos of the rig on the odd thread, if you'd like some pics lmk & I'll put some up here as well.
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