I'll see if I can help you.
OK, let's draw a box...(now, since we're going to cut a hole in this box, you might want to make sure to "Set Surface Type" (bottom left of the interface) as a 2-sided-surface box, so that what's inside will show once another object is cut out of it
Then let's draw a cylinder, which we want to make a "hole in the box" with using Boolean Subtraction.
We open up Boolean Operation from the Tools menu...
Select the "operands", or the objects involved in the operation. Since the operation we're using is "B Minus A", we select the box and then press Set next to the Boolean B space; we select the cylinder and press "Set" next to the Boolean A space.
Now, we decide whether we want to delete any of the original items. We definitely set the cylinder to be deleted since we're only using it to shape the hole. You may or may not want to delete the original box; you might want the original to 'hide' and use as a reference... you may just want the box with a hole only, in which case you might check that box to be deleted.
Click OK.
Now, view the results. (I have the pink "Normals" lines visible here so you can see which way the polys are facing). Note the resulting object is usually given some odd name like CSG0; rename the object to something that makes sense to you.
Now you see the results... and you see why using Booleans is sometimes very messy. Sometimes you may have to select some surfaces and delete them to truly uncover the hole (especially if you did not Delete the original box). It may be wise to find groups of polys to combine and realign to save complexity and vertice/poly count. These are likely formed because of the differences in the geometries and how their respective vertices line up.
Sometimes, Booleans will make such a mess that you'll want to, in this example, select and delete (surfaces only!) all the internal surfaces, and redraw the inside of the hole one 3-sided surface at a time. Or, if your shapes are not very complex, it might be better to just subdivide the object and use negative extrusion to get the hole or missing area you want and delete it.