How are quarterly tax installments accounted for in Moneyready

I realize this is not an accounting program, but I am trying to get the best estimate of our years' cash flow in retirement.

The TIME MACHINE calculates your taxes for you, so do not enter taxes in Expenses, even quarterly payments.
What’s very important is to capture the taxes you’ve already paid this year in the screens that capture that, right before running the TIME MACHINE.  It needsto know what you already paid so that it can credit you. 

Taxes and deductions paid year-to-date (at source taxes, CPP/QPP and EI contributions, tax instalments)

For the current year in the TM, it shows you the expected cash flow from today to the end of the year. 

That is: what expenses are left to pay, incomes to be received, taxes left to pay.

In the detailed year report for the current year, the taxes shown are then the total taxes minus whatever you’ve told it you already paid.

It may show you that you'll get a refund.