Examples, with amounts?

I usually check the "let IRS figure it" box because it's usually under $100 and they don't assess it. 

If the penalty can be reduced by using one of the exceptions on the 2210, I'll do that.  That often eliminates the need for the July 15 payment entirely.  But I might hear from a few clients.  

If the client insists on paying the penalty with the return and it's obviously high enough that IRS will assess it, I go along with the Pro Series calculations.  Staying tuned for calls from clients who won't be unhappy about a small refund check.