The best way is going to
/usr/share/applications on Nautilus (or your favourite file browser). Then open gedit as root.
Select any .desktop file and drag it to gedit (obviously you can open it in several different ways, but I this is specially quick for me). You will see the .desktop file content, the interesting thing it that:
If the icon name is only «someapp» and it doesn't specify any special location, it will use your selected icon theme; this is great, because it will use all sizes.
You can type add an extension format so that it will only use this format, but in all sizes.
If you specify the path, it will only use that specific icon and only its size, e.g,
Icon=/home/user/niceicons/cuteicon.png: if the icon is 16x16 px, it will be aweful when showing it in the Unity panel, for instance, which doesn't happen when you use a .svg (Scalable Vectorial Grpahic, wich addapts to any kind of size).
I prefer this way instead of the GUI way, because it's clearer what are you putting on the .desktop file.
Hope it helps you ;)