That’s one of the big advantages of The Queue.
If you have to render two separate files/movies/whatever, adding a second output module to the same Render item is the best way. One Render Setting, multiple Output Modules. When you push the render button, AE renders a “pure” frame at the Render Settings, then compresses (or otherwise alters) the frame twice to suit each Output Module, then it moves on to the next frame.
This is faster than setting up two render queue items, because the rendering time is actually spent in the Rendering of the initial “pure” frame, not in the compressing to the desired file format.
Of course, for example, if you need a progressive version and an interlaced version, you have to set up multiple items in the Queue, since they both have different Render Settings. Such is life.