Are they cubes or chips? If they are chips, they need very little contact time, at least to me. When I use chips I use a lot, like 3-4 ounces and only soak for a couple of days not even a week. It does take some time for the oak to die down to the level I like I find chips give a real sharp oakiness. If its cubes (which I prefer a lot more flavor wise) then yes you would want the beer to sit on them for at least a few weeks. And yes you can pour the bourbon in the secondary along with the chips if that is what you are soaking them in.