I never ended up getting a useful answer on here, but I did end up figuring it out the next day. My box was being drawn using coordinates that were from -1 to 1. But my click had large screen coordinates such as 200,300. I needed to know how to convert the -1 to 1 into screen coordinates, or how to just draw it compatible coordinates.
glMatrixMode(GL_PROJECTION);
gluOrtho2D(0, 400, 0, 400);
glBegin(GL_QUADS); // Box
glVertex2f(xOffset + topBaseX + -15, topBaseY + -15);// bottom left vert
glVertex2f(xOffset + topBaseX + -15, topBaseY + 15); // top left vert
glVertex2f(xOffset + topBaseX + 15, topBaseY + 15);// top right vert
glVertex2f(xOffset + topBaseX + 15, topBaseY + -15);// bottom right vert
glEnd();
glLoadIdentity();
That was all I had to do to draw my box at something like 200,300 and then I could simply check the boundaries of my box on each click.