Preparation of rye grains

I've embarked on a third bake of a great rye recipe. The original site seems to have died, but thankfully there is a copy at the Internet Archive.

The recipe calls for "250 grams of rye grains" and says to add them at the start of the first bulk. I tried that, and the seeds were too tough by far in the baked loaf. I tried a second time, soaking the seeds for about 12 hours and it didn't make much of a difference.

Having looked around here, I think I want to try cooking the seeds first, so I have two questions.

1) Would you add 250 grams of cooked seeds?

2) Or, would you cook 250 grams of seeds and add that?

Thanks

Jeremy