First I'm going to explain the nature of the software. The software is based on Inflows and Outflows. With 'Income' used to model any inflows into the accounts and 'Goals (and Fees)' used to model any outflows from the accounts. So for example, Payroll, Social Security, and Pensions would be the inflows into the account. And any outflows such as expenses, expenditures, or retirement spending needs would be set as a 'Goal' (or outflow from the account).
The system’s primary objective is to satisfy the 'Total Net Goals and Fees' (column 5 on the cash flow report). To satisfy the 'Total Net Goals and Fees', the software will first look to 'Total Net Income' (column 4). If 'Total Net Income' is less than 'Total Net Goals and Fees', the system will then look to satisfy the difference from (in this order): 1) Taxable Accounts (column 7), 2) Tax-Deferred Accounts (column 8), and lastly 3) Tax-Exempt Accounts (column 9).
The 'Beginning Portfolio Value' (column 3) in Year 1 (2018 for example) is just the value of all the accounts added together. Anything taken out of 1) Taxable Accounts (column 7), 2) Tax-Deferred Accounts (column 8), or 3) Tax-Exempt Accounts (column 9) will reduce this value. Any contributions or excess income will increase this value. The 'Simulated Net Return' (column 13) will also change this value.
Here is an article for a complete breakdown of the cash flow report. Scroll down to Report Output: