Render Layer Effects

Such an approach makes zero sense. Even if you flatten some effect results, the mere process of reading a file, applying an effect and writing another file could consume just as much resources or even more, given that decompressing files also causes tons of file I/O overhaed for cache operations.  Complex interactions with other layers or limitations in how some effects work could also fully negate any advantages or at the very least complicate your workflow in unexpected ways. A typical example would be anything with 3D layers, naturally. If at all, pre-rendering only makes sense on a comp level when you know the result isn't going to change anymore and the resulting substitute clip is more or less used directly in other comps. Beyond that it's moch more sensible to rely on AE's internal optimizations and structuring your projects suitably. That will ultimately do more for you than trying to circumvent functions.

Mylenium

There are very few cases where this would be an advantage. One would be a fairly long clip that had warp stabilizer applied, but then again, if you are warp stabilizing footage that has some kind of visual effect or graphic added to the shot that is using motion tracking, you should motion track, add the effect, then pre-compose or Render the comp, and then apply Warp Stabilizer to the pre-comp or the rendered production master so that the effect gets warped the same way the rest of the shot does. 

That was probably confusing to a new user, but the point is that it is very unlikely that you will save any time by adding a few effects, rendering, then adding more effects. 

We need to know your workflow and design goals in detail to give you good suggestions on workflow. 

If you really must render an intermediate file you should NEVER use the Media Encoder to render an MP4. You should use the Render Cue and render a lossless or lossless with alpha file using the presets in the output module. Don't go messing with rendering presets unless you have become somewhat of an expert in video formats, standards, and compression. You'll just get into trouble. If you open up the options by spinning down the Output Module twirly (>) in the Render Cue there is a button for Post Render Actions. Choose Render and Replace Usage. This will render a DI (Digitial Intermediate) Import the file into the project, and replace any instances of the comp you rendered with the rendered file.

You should also be very warry of YouTube tutorials. Most of the new ones are presented by enthusiasts and most of them have problems explaining what they are doing and a lot of them give advice that is frankly, terrible. You should spend a fair amount of time with the Learn resources in the Home Screen of AE, make use of Adobe's User Guide, available on the AE product page and in the help files, and you should probably search for answers to questions first using the Search Help field in the top right corner of AE. You'll get answers that are at least vetted by Adobe and most of the links that show up are pretty good.