Is there any way to account for two VAT-type taxes in purchase and sales documents? In Canada in some provinces there are 2 sales taxes : one on a federal level (GST), second on a provincial level (PST). In some provinces they are combined into one tax called HST.

Not as of today.

We are currently redoing our tax calculation engine and integrating with Avalara.com for that. They do provide tax calculations for Canada too.

Specifically this is what you are asking for:

http://developer.avalara.com/api-docs/best-practices/document-lifecycle/gettax/detaillevel/

Please send me a private message and I'll be able to update you on the integration status.

Best,

Konstantin