Add samples by clicking on the Add Sample button in the workspace (left most function button).
You can also add sample files (or folders of sample files) by simply dragging and dropping the files from an Explorer window, the desktop, etc. to the Sample area of the workspace window (in blank Workspaces, you'll see Drag Samples Here in the background of the Sample area of the Workspace).
Upon clicking the Add Sample button, you will be shown the standard Windows Open File dialog. You can add a single file by opening that file directly. If FlowJo determines that this is an FCS file, it will add it to the current group (shown below)
Alternatively, you may select a folder and click on the button Add all files in folder. FlowJo will then look at every file in the folder you specify. If it is an FCS file, it will be added to the workspace. In addition, FlowJo will create a new group that has the same name as the folder you selected; the files you just read in will be added to the folder. This way you can add an entire experiment at once! If adding a folder to the workspace, FlowJo will add each subsequent folder contained therein as a new group.
