Unfortunately I think you have to add the 5% to the existing line discount.
Line & invoice discounts don't appear to play well with each other.
$1.00 * with 25% line discount = $0.75
($1.00 * with 20% line discount) * additional invoice discount of 5% = $0.76
You can always add a comment line that says "Additional %5 Discount has been applied to this order"