We usually fill the dropper with some of the oil and then run warm water over it for a few seconds from the faucet. That warms it up nicely. Our doc (a naturopath) has always had us do 3 drops, in affected ear(s), 3 times a day for 5 days. I usually let the oil go into the ear canal and then jiggled it a little to get it down in there and then if I can get my DS to sit still keep the ear pointed up so it gets a chacne to roll around in there. When I've had to do two ears I have always put a little piece of paper towel under the first ear when I turn my DS to do the second because some oil always runs out.
I don't know how old your son is but if you are still BFing, you can also put breastmilk in the ear and that can help too. For a little while we thought my DS was allergic to garlic so when we suspected ear issues we'd do breastmilk in the ears.
Wife to DH, Mama to DS1 (06/2007) and DS2 (06/2013), missing babies (mc 08/2006 @ 5 weeks) and (missed mc 06/2012 @ 11 weeks)