Many customers wish to use a Subwoofer when mixing or listening to Stereo audio.
The User Manual for the Pro 40 or 18i20 will instruct you on using the 2.1, 5.1 and 7.1 setups for when using Multichannel audio, but most people are not using Multichannel audio. Most customers are using simple Stereo audio, such as a regular YouTube Video or Song, rather than a Blue Ray or doing a full 5.1 mix in their DAW.
You will know if you are using a Multichannel Mix in your DAW as you will see 6 channel in the Master Fader, rather than the normal 2 faders. Your program will also be looking for 6 channels of Output, rather than 2.
If you want to use a Subwoofer with Stereo Audio you will not hook it up to a separate Output on your Interface.
Most commercial Subwoofers are designed to accept the Stereo full range output for Left and Right and then send the approriate audio to the Monitor Speakers.
Here is a diagram for setting up a common commerically available Powered Subwoofer.
If you are using a Multichannel format audio where the audio being sent to the Sub or LFE is already not full range you will use the setup described in your unit's Manual.
If you have a passive subwoofer/speakers you would generally also be using an amp or home receiver to provide power to the speakers, so the Stereo Line Outs would go to the receiver's L/R inputs. The receiver would then act as the crossover/amplifier to the sub/speakers, splitting the audio properly.
For Scarlett 18i20: http://d3se566zfvnmhf.cloudfront.nethttp://d3se566zfvnmhf.cloudfront.net/sites/default/files/focusrite/downloads/8424/scarlett18i20-user-guideeng.pdf
For Saffire Pro 40: http://d3se566zfvnmhf.cloudfront.nethttp://d3se566zfvnmhf.cloudfront.net/sites/default/files/focusrite/downloads/7046/userguidepro40english04_0.pdf
For Liquid Saffire 56: http://d3se566zfvnmhf.cloudfront.nethttp://d3se566zfvnmhf.cloudfront.net/sites/default/files/focusrite/downloads/7092/userguidels56eng_0.pdf
If you have further questions please Contact Support.