They are different types of Essential Fatty Acids and both are needed for good health. I'm not sure about dogs but in humans we need a high ratio of Omega-6 to Omega-3. A lot of people are deficient in both EFA's but especially Omega-3 because our diets on the whole are lacking in oily fish (the best source of Omega-3), so many would benefit from supplementation of both types of EFA but in a ratio that favours Omega-3 to tip the balance back to good health.
Hope that makes sense.
Hopefully Tohme might be along to explain it better. :)
Kath.