You can put them in a hop bag, grain bag, (or paint strainer bag--what I have started using) or you can just throw them in. If you do just throw them in you have to have a way to strain them out. Most of my brews I have just thrown the hops, grains, etc in and strained them out. This will lead to a less "clear" beer--but if you don't care about aesthetics (which I don't) then go for it.
so whether you eat or drink, whatever you do, do it all for the glory of God.