Just wanted to share a solution I'd found to a problem. As a company that imports and exports a lot, I receive a number of customs brokerage invoices where the GST/HST assessed is the majority of the invoice. Also, we occasionally have some smaller purchases where there are some charges with HST and some without (coffee and cream).
First, I tried a number of different tax options combinations, but whenever I edited the HST amount, it would change the expense total by re-calculating my other entries. Auto-calculate is fine, but sometimes I just have to override it.
The solution I've found that seems to work is to set the bill/expense as "Exclusive of tax", then the line item(s) as "Zero-Rated". Enter the subtotal before tax. i.e. $15 brokerage fee. This will bring up the HST box between the subtotal and total lines with a temporary value of $0. Now you can enter the amount of HST, i.e. $54.63. The bill/expense will now show a total of $69.63 and match my invoice. When saved, it will now appear in the HST reports and be included as an Input Tax Credit correctly.