As per the HST FACT Sheet issued by CBSA: http://www.cbsa.gc.ca/media/facts-faits/081-eng.html

"As is the case today, the provincial component of the HST will not generally apply to commercial goods that are imported by an HST registrant for consumption, use or supply exclusively in the course of the commercial activities of the registrant.

Although the provincial portion of the HST is not payable when commercial goods are imported into Canada and destined for a participating HST province, the goods may be subject to self-assessment rules. For more information about the self-assessment rules, please consult the Canada Revenue Agency (CRA) Web site at: www.cra-arc.gc.ca." or, call the Canada Revenue Agency at:1-800-959-5525

What does this mean to a Commercial Importer?
When importing goods for "Commercial Purposes" the B3 document will only reflect the 5% Federal portion of the HST. Like the PST before it the 8% Provincial portion of HST "will not generally apply to commercial goods". However, some commercial goods may be subject to the 8% portion of the HST and the Commercial Importer would then be required to "Self-Assess".

Self-Assessment 

If a Commercial Importer is required to remit the 8% Provincial portion of the HST to CRA (Canada Revenue Agency) then they must "Self-Access" which means keeping a record of the 8% portion of the HST calculated on the "Value For Tax" required by CRA on any subjected Commercial imported goods. It is the importers responsibility to track and calculate these taxes and then remit them to CRA 

Self-Assessment Rules: http://www.fin.gc.ca/n10/data/10-014_1-eng.asp#_Toc252889034

Please Note: It is the Importers responsibility to contact CRA to confirm if they are required to "Self Access" the 8% portion of the HST. 

Canada Revenue Agency (CRA) Web site at www.cra-arc.gc.ca. or, call the Canada Revenue Agency at:1-800-959-5525