On my extension request, I entered $25,000 as my total tax liability and $0 as amount paid to get to my estimated $25,000 left. In reality both #s should be 100K higher.

You do not need to send another Form 4868.  The only amount that matters is the amount you pay - it needs to be enough to pay your tax liability to avoid penalty and interest.  Those other amounts are just "estimates", and aren't used for anything.