To set up the new HST's is pretty simple. I'm breaking all my provinces down independently just so every time a province changes their tax rates it's easier to adjust. This is assuming that you followed the original excellent tutorial that Dr. Byte created and you have the two classes "GST/HST/PST class" and the "GST/HST/PST on shipping" class.

So I'll take Ontario as an example, and just do each province accordingly:

Under "Locations/Taxes" go into "Zone Definitions". Create a new Zone.
Titled: HST - ON Description: HST for Ontario
Once you've created that, it will have a red dot beside it. Click on "details" then "insert", and choose Canada then Ontario out of the list. Now your dot should be yellow.

Under "Locations/Taxes", go into Tax Rates. Click "insert new rate"
Choose PST/HST/GST class
Zone is the HST - ON
Tax Rate - 13%
Description - 13% HST
Priority: 1
Then click insert

Now you have to do the same thing, just choosing the class as "PST/HST/GST on shipping" class and make the description 13% HST on shipping

Now go back to your original "Zone Definitions" and remove ON from what ever definition you had it under previously. Do this by clicking on the definition, choosing "details" and deleting the province from the list. At his point your dot should now be green since it has all been set up. Run a test order and see how it goes.