My setup is this;
5 Apiaries. Two of those have Industrious Bees in, the other three have Imperial, Heroic, and Soul respectively. Those are just the five I chose to use, and Soul takes a while to get, plus you need to adapt them to the climate as well. They're all pure breeds though.
I have all the apiaries automated so that when the queen dies, the drones and princess loop straight back into the apiary in a neverending cycle. It works so well with the trees, that I managed to get 4 Common Walnut Saplings in 10 minutes today. I've just planted Mundane Larch and Bull Pine to get Coast Sequoia saplings, which I now have 3 of.
But the point is that yes, Pure Breeds work incredibly well for cross-breeding trees.
One thing I forgot to tip you on last post. Say for example you've planted 3 Silver Limes, and 3 Hill Cherries. Make sure they alternate, so that the pollen is more likely to land on a different tree breed.
Edit: Well, after another 2 hours of playtime, I managed to get my 9 Coast Sequoia saplings, and Grafting just one grown Sequoia got me another 192.