Need to file an extension and I am making the assumption it is better to overestimate taxes owed than underestimate to avoid penalty?

Yes, there is no penalty for overpaying on on your extension. When you do eventually file your return, you'll simply get a refund for any over-payment. However, if you underpay, then you run the risk of being hit with interest and penalties.

Please Note

• If you underestimate the amount of tax you owe, you'll have to pay interest on whatever amount you fail to pay by April 18.
• If you do not file your return or extension by April 18th, you will be subject to late payment penalties - 5% of the amount you owe for each month of late payment, up to a maximum of 25%.
• If you pay less than 90% of the tax you owe, you'll end up owing a penalty of 0.5% of the underpayment every month until you pay the balance.

Please see the FAQ below for amendment instructions. https://ttlc.intuit.com/replies/3301328

I am thinking of making a second payment via the IRS direct pay site (extension) in case I underestimated. Is this a problem to issue two payments? Or should I pay right after the 15th to avoid it getting confused which payment is which? If I pay after the 15th I don't know what to code the reason to be. I am waiting for my return to be reviewed (using TT Live) before I file it. thanks

There is no harm in making multiple payments, they will each have different tracking.  They are similar to estimated payments made throughout the year in that you will reconcile them when you file, with any overage refunded to you when the return is processed. 

@gumbootkitten