You can customize the invoice layout by modifying this file : Mage_Sales_Model_Order_Pdf_Invoice(app/code/core/Mage/Sales/Model/Order/Pdf/Invoice.php). Of course you need to rewrite the file properly.
Also take a look at these articles for additional info and examples:
Best Answer
Go to
Set
Display Full Tax Summary
to Yes and save config.This should add the tax percentage to Magento's PDF Invoice. You can see the difference below.