Leder Gris (or, in English, Leather Grease) should be applied using your bare hand and fingers all over the leather portions of your boot, working it into the leather and paying particular attention to stitching and any joins and creases. Remove the laces first and pay attention to the tongue and bellows. The warmth from your hand will warm the grease up and help the leather absorb it. If your a little messy, try not to get it on the soles, particularly if your going to drive soon afterward.
Alternatively, buy Nikwax Aquesous wax and, using the provided sponge applicator, apply, leave three minutes, then wipe off. A tip for you, use neutral Aqueous Wax, black is OK for black boot's, but it can make a bit of a mess, neutral is far better, because you cannot see the mess!