Sorenson Squeeze is a very flexible tool that can take almost any format and convert it into a format that is suitable for the delivery of videos to a target that you've specify. With Squeeze you can also create so-called watch folders. If you copy a video to a watch folder, Squeeze can automatically take the video, process it, and upload it to a destination of your liking.
First download this preset and import it via Preset => Import… This new preset should now show up in your favorites.
In our default preset we encode to 720p at 5000 kbps. If your video is only SD, you can choose to lower the frame size to 720x480 and lower the data rate to 2000 kbps and still get good quality.

You can now create a new publishing option by pressing the little + sign in the publishing options panel on the left side of the screen.

In the screen that appears, add the following settings:
Now all we need to do is add Bits on the Run to our imported preset. All you need to do is drag and drop the Bits on the Run publishing option onto the Bits on the Run preset.
To encode to Bits on the Run, all you need to do is drag and drop the Bits on the Run preset to the button right hand panel, which is the job queue. The Bits on the Run profile will now be applied to any file that you import.