Beginners After Effects Workflow questions

Rendering digital intermediates (DI's) using a Mezzanine format or codec (I'm using industry-standard terms here) is a common practice and if you are at all serious about quality, you should follow that workflow.

A DI is a visually lossless format that is frame-based. The general distribution format right now is an H.264 compressed MP4 file that is 8-Bit, RGB (no transparency possible) inter-frame compressed format that has to contain color artifacts and compression artifacts because of the way it used predicted frames to generate most of the pixels in a movie.

Make sure you understand that. An MP4 is not designed to be re-compressed or used again in any way in the production pipeline. Many consumer cameras use MP4 files for video recording, but they are consumer products, like mobile devices and consumer cameras. Some of them make amazing images, and in a lot of cases, the footage can be used in professional productions, but the MP4 file format should never be used as a DI.

A Mezzanine format or codec is a visually lossless, frame-based format that uses interframe compression and every frame can stand on its own. Mezzanine codecs are usually capable of 10-Bit or better color and RGBA color space. These formats include image sequences, ProRez, GoPro Cineform, AvCHD (Avid), and other similar formats. Production facilities all have their favorites. I worked on films last year that wanted Tiff Sequences, Go Pro Cineform, Red, ProRez 444, and EXR sequences, so that is what I delivered. 

For my own workflow, I have edited the Output Module Templates to use GoPro Cineform 10-bit RGB for the Lossless preset and GoPro Cineform 10-bit RGBA Straight Alpha for my Lossless With Alpha and my Pre-render default formats because the format is excellent, universal, has a reasonable file size, and it works. I would strongly suggest that you study up on video formats and use the Edit/Templates/Output Module menu and edit your own set of presets.

My rule for Dynamic-link from and to Premiere Pro is as follows: If the comp will render at the rate of several frames a second I will use Dynamic-link. If render times are longer than 2 or 3 frames per second I always Render the file and replace it in Premiere Pro. I should tell you that I often have comps that take a minute or more a frame to render and if the render time exceeds three or four minutes I start thinking about redesigning the composition. I also Pre-render and replace usage all the time if I am using Rotbrush, Warp Stabilizing, or rendering complex particle or 3D projects that are nested in my main comps.

I also often render everything but the background layer when I do composites. Here's a sample video from a project I am working on for a new tutorial series.

The project is about 1/3 of the way to being complete. It is a day for night, motion tracking, insert elements project that will go into a short film edited in Premiere Pro. Here are screenshots of the Before/After/and Rendered output that is going into Premiere Pro. 

I am not rendering the entire composite, just the parts that are filling the holes in the final shot because the final color correction will require separate control of the background and the overlay to get the exact look that is required. It would be way too difficult to do the final color grading if the pieces were all on one layer. 

I hope this gives you some guidance. 

For rendering your deliverables be sure and check out the User Guide. There are a couple of good rendering tutorials there. Don't mess with the settings until you get a good understanding of video standards, formats, codecs, and compression.

As long as you don't need to make text edits to the AE file in Premiere Pro, nothing wrong with rending the AE comp first and placing in PPro. 

If you are using transparency, be sure to use a format that supports it. I use AVI with RGB+Alpha, but there are other formats too.