Click the Save tab at the bottom of the window to launch the saving dialogue. Alternatively, you can access it through File / save-export.
If you choose to transcode a file at the Start screen, you will also skip right to this dialogue.
Click the Browse... button to select the destination path. Make sure to not rewrite the original file (unless you want to).
There are several preset options. These settings are optimized for the best accessible quality/size ratio.
You can also select the Custom ratio button and choose from more optimized presets of various filetypes. To define your own settings, click the Change... button (for advanced users).
In the Custom Format dialogue you can: