Do quarterly payments need to be equal?

[iEngineer]

My income has increased from last year. I already made my first two estimate payments based off the safe harbor method. Will it cause any issues to increase the payment amount for my next two payments? 

If I mis-calculate and fail to pay 90% of the total tax due will I owe a penalty. Or would it be waived since I still paid more than last years total tax?

[CatherineR]

Great job keeping on top of this iengineer!

You can adjust the estimated tax payments as the year progresses.  It can't hurt to have more paid in and if you file as early as possible it will come back in your refund.

As for penalties if you underestimate, there are a few safe harbors to use and Turbo Tax will check them all to make sure you do not pay penalties if you qualify.  

Here is a great IRS resource that discusses underpayment penalties 

Underpayment of estimated taxes