Although this question might seem to be trivial, you should clearly understand that your portfolio consists of open positions (stocks you possess).
Your portfolio AND available cash at your brokerage account make up your Total Capital - major indicator for every investor.
Example: Lets say that you have $10,000 invested into stocks and plan to invest another $5,000, your Total Capital is $15,000. PortfolioRunner will give recommendations based on calculations made considering your available cash. Sure, you will be able to adjust this amount at any time. Buying stocks will deduct available cash and selling will increase the amount.