Well... I'd put the pins in an orientation so I could read the writing on the board when it was plugged into whatever.
If you're placing it on a breadboard or a PCB, it is fairly intuitive that the pins should be placed through from the rear side of the board and soldered on top. If you do it this way you'll need to be sure that the pins clear the battery that's mounted on the rear side of the board.
However if you're (say) hot-gluing it to a surface (again, consider the battery) and you intend to run patch cables to (say) your arduino, then it would make sense to place them in from the top and solder them on the rear side.
As to whether you need the SQ pin, the answer is "only if you need it". Check the datasheet for the DS1307 and see what it's used for (hint: it produces a square wave output). Do you need that? If you're using a sketch that someone else has written, does it specify a connection to this? This is not a question that has a yes/no answer.
