A "closed surface" is a surface that completely encloses a volume of space. The 6 faces of your box, all together, make a closed surface; i.e., they completely enclose a volume of space (the inside of the box). An individual face, such as the top of the box, does not represent a closed surface. A closed surface can have any shape as long as it completely encloses a volume. The surface of a balloon is a closed surface even if you deform the shape of the surface by squeezing the balloon.
For any closed surface, no matter what it's shape, the total flux through the entire surface will be zero for a uniform field. This assumes that you adopt the sign convention for flux mentioned earlier. (The flux through a closed surface might be zero even if the field is not uniform, but you'll learn the conditions for that when you cover Gauss' law.)
So, the total flux for the entire surface of your box should be zero if you consider the signs of the flux for the individual faces. As a check of your work, you can see if you get a total flux of zero.