A Fund Manager portfolio is a collection of investments, sub-portfolios, and all of your preferences, such as window positions, colors, fonts, displayed reports, etc... A portfolio is saved to a file with the extension of *.mm4. A portfolio can be thought of as your complete workspace.
A portfolio can have an unlimited number of sub-portfolios. Sub-portfolios can be hierarchical, with no limit to the depth of the hierarchy.
Sub-portfolios include investments. When you open a portfolio, the included investment files are opened as well.
Advanced: Portfolios store their included investments with a "relative" path and filename. The stored path and filename are relative to the location of the portfolio's *.mm4 file. This makes it convenient to move the location of your investment and portfolio files, without having to update your portfolio. For example, if a portfolio at C:\Data\MyPort.mm4 contains an investment C:\Data\BrokerA\IBM.dat the location of this investment would be stored in the portfolio file as .\BrokerA\IBM.dat. This way, if you need to move all your data to a different folder, as long as you keep all the files in the same relative location, everything will be transferred seamlessly. See Common Portfolio Problems for more discussion on this.