Good follow-up questions. First, the PHEV credit is applied toward your tax liability, meaning what the tax is calculated to be based on your taxable income regardless of what you may or may not have paid toward that liability throughout the year. Then, any underpayment penalty is calculated based on what you still owe and when you made payments throughout the year.
So, let's say your taxable income is $100k and the tax liability is calculated to be $10k (purely random number) and you paid $5k already during the year. The tax calculation reduces that $10k by the $6k credit giving you $4k that you still owe. Because you already paid $5k you will get $1k refunded to you.
To be clear, that $1k refund is from the excess you paid. If your tax liability was calculated to be only $4k then you would only get $4k of the credit toward the liability where you would get all of your $5k back in a refund, meaning none of the refund is attributable to the credit. I hope that all makes sense.
Having said all that, if you are more comfortable making some estimated payments that is fine. You will just get any excess back when you file.
