Capture can be configured to handle multiple lines with multiple VAT rates, however, if the system has not been setup this way then the best way to deal with this is:
Sum the individual VAT totals and enter this as the VAT value for the invoice, keeping the VAT rate as 0.00.
Verify the invoice as normal.
In the software to which the invoice details are exported, locate the invoice and add/update the individual detail lines along with their appropriate VAT rates and amounts.
Contact your customer success manager to discuss reconfiguring Capture to handle this as part of its normal operation as there may be other factors to take in consideration.