In my opinion crates are the best way to go. The newer ones are nice, with the movable/removable divider, as the pup grows so does the crate. I get them used to the crate being a wonderful place by tossing dog kibble in there, with a young pup you may have to start with a sort of trail starting on the outside, leading in. Toss treats in there on occasion when they are out, they will make a habit of checking the crate once in a while.
Some dogs get used to being crated overnight quickly, other make a big fuss. I have a little trick I've done with my last two dogs, one is nearly 1 1/2, the other is just shy of 4 months. I fold up a comforter, toss it on the floor next to the crate, along with a pillow & blanket, and crash with the pup. After about a week they get used to the routine, seeing the same sleeping gear. I then set up my sleeping area by the crate, and go sleep in the bedroom, the pup assumes I am there.
Clicker training works great for house breaking, the pup is nearly housebroken, I'm not going to jinx myself by saying he is, as he is doing really good.