Difference between Render Settings and Output Modules

Render Settings tell the rendering engine what to do with your comp. The Output Module tells the rendering engine what codecs to use and where to put the rendered file. Until you are an expert in video formats and compression you should not mess with the presets. Use them. They work. The same thing goes for the Render Settings. The presets are available using the pulldown. 

The default Best Settings will give you a render that matches your comp's dimensions and frame rate, the quality will be set to full, the in and out point for the render will be set to Work Area, and it will use the current settings for all layers. More than 99% of the time, you should not have to change these settings. You just have to make sure that the Work Area is set to the in and out points you want to have for your comp.

The output module defaults to lossless, which will give you a frame-based lossless copy of your footage you can use as a production master in Premiere Pro or for further work in After Effects. This will be a large file and it is not suitable for sharing or uploading to streaming services like Premiere Pro. If you need a production master with an alpha channel (transparency) use the Lossless with Alpha Preset. Most of the render problems people have with the render cue I see on this forum are caused by people that don't know what they are doing fiddling with the controls. Just use the presets until you gain the required knowledge. 

There are tutorials in the User Guide, available on this forum, the After Effects Home Screen, and the After Effects Product page that goes over rendering for sharing. They use the Adobe Media Encoder. The same rules apply, use the presets, don't monkey with the knobs. 

And no - codecs have nothing to do with frame rate, and Quality in the Render settings has nothing at all to do with compression.

This page somewhat helps me, but it's still not clear why we have separate areas for Render Settings and Output Modules. I see that Render Settings decide quality and frequency of frames, Output Settings decide which codec is used, but isn't a codec also deciding quality and frequency of frames?