There should be a Data Browser pane on the left side of the Linear Analysis Tool window. If you can't see the pane, then you might need to click the Data Browser tab on the left edge of the window and Restore it. Once you have the Data Browser open you can click and drag variables from the Base Workspace into the Linear Analysis Worksapce or go the other way. If you're working in the base workspace, you can make your Bode plot at the Matlab command prompt:
If you want to work in the Linear Analysis Tool, highlight the variables you want in the Data Browswer -> Linear Analysis Workspapce pane and then select the plot you want under the Plots and Results tab.