I use sunflower seeds, caraway seeds, flaxseed and millet as well. You just throw them into the mix and let the breadmaker do its thing. Go easy on the caraway seeds though since they have a very strong taste and many people don't like them. But seeds are full of omegas (you knew that already though!) so they are really good for you.
I do add sunflower seeds and linseeds, that was until I realised that linseeds pass through whole. So now I add LSA mix (ground linseed, almond and sunflower seeds). My mother adds Flaxseed oil to her breakfast, supposed to be very good for you, but I'm not sure about adding an oil to muesli.
I haven't tried caraway seeds.
Millet is one of the finest foods available. It will grow where other grains won't, it has a protein level akin to that of wheat, and it's full of vitamin B, including the controversial vitamin B17.
I hadn't heard about B17, until talking to my cousins son, who was researching it when his mum was having chemo. There was something about that it may conflict with chemo. Apricot seeds seem to be the best source of B17, but quite bitter.