.. Flour can absord someting but with seeds I think it is different..
I put them on when I prepare the bread before its last time rising: the toplayer is a little sticky and it will slightly sink in and with baking it will get 'attached'. I think that is all you can do. Even when you get a loaf of bread from a good bakery you lose quite a bit when you start to cut it. (I worked in an organic bakery for a few years; using a machine you lose at least half).
Depending on how wet your dough is (there is some space between to wet and to dry: see where you are), you can paint some water over the top after the last knead, then put on te seeds. Make sure you don't touch it anymore before you put it in the oven.
When you bake someting and you add heavy things (apple, currants) and you don't want them ending up at the bottom you mix them with flour before mixing them through your dough (I mean the doughs you can stir, not knead like soda bread or cake), but that ofcourse doesn't work for a topping.
Have you ever tried baking in a 'closed shape'? Your bread wil hit a top and the seeds will be pressed in.