This is the first step after you get both layers back into a cube shape.  This step is very intuitive.  The basic idea is to try and pair up two corners (often times, you will already have two corners paired up) and put them on the bottom left side.  Then you have to separate your other two corners (in other words, get one on the top layer and the other one on the bottom).  Then simply pair them up on the top layer and insert them into the bottom.  If you're having trouble doing this on a Square-1, try it on a 2x2x2.  Orient your corners and try to solve the bottom face using only R2, U, and D turns using the same process described above, and it should start to click.

Sometimes, you will run into a situation where all of your bottom corners are already on the bottom, just not in the right places.  You have one of two cases here.  If you have two corners that are paired up, put them in the back and perform this alg:

/ (-3,0) / (3,3) /  (0,-3) /

If you do not have any corners that are paired up, perform this alg:

/ (3,-3) / (-3,3) /

Note that that alg can be performed from any angle.

That's pretty much all there is to this step.  It's very simple, and it usually takes 3-5 twists.  It should never take more than 6 twists as far as I know.