If the file is a CSV file, you can specify a column for the VAT rate. Is that what you’re looking for, or more for specifying the exact amount of VAT charged?
There’s a full list of supported fields here:
http://community.quickfile.co.uk/t/importing-sales-and-purchase-invoices/8885
Another option may be to use either our API (a developer can set this up to link your client’s web based shop straight into their QuickFile account to generate invoices etc.), or to look at a tool like Zapier.