To save changes to your portfolio properties use the Save Portfolio command from the top level File menu. You can also select the button from the toolbar. To save a portfolio to a new filename use the Save Portfolio As... command.
Saving a portfolio is independent from saving investments. When you save a portfolio, you are saving which investments are included, the sub-portfolios, and all of your preferences, such as window positions, colors, fonts, displayed reports, etc to the portfolio's *.mm4 file. When you save investments, you are saving any pricing/transaction data to the investment's *.dat files.
To have your portfolio automatically saved each time you quit, see the Save Portfolio on Exit command under the top level Options menu.