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I use a workflow that has me cutting in PP then sending whatever needs CC or motion graphics to AE using the dynamic link which is solid in CS6. Read up on dynamic link for more details.
Let's define some terms first:
- Shot: A continuous block of unedited footage from a single point of view. Also called a Take.
- Sequence: Two or more shots that that have been trimmed or cut together to tell a story.
- Scene: A continuous block of storytelling either set in a single location or following a particular character. The end of a scene is typically marked by a change in location, style, or time. A scene can be a single shot, a simple sequence, or a combination of many sequences.
- Movie: A completed project that tells a story. A movie can be 10 seconds long, or 10 hours (re: Andy Warhol)
The best use of After Effects is to work on a Shot, Scene or sometimes a Sequence, to composite elements, add graphics, or adjust the look (color grading) of a Shot or a Sequence. After Effects is probably the most difficult tool you could ever choose to edit a long form movie. Dynamic link is very useful in the early stages of developing sequences. Once the sequences are approved, I will usually render the sequence to a production codec for use in the NLE. I'll talk more about codecs later.
The best use of Premiere Pro (or any NLE) is to organize shots into a sequence or scene, and then to organize the scenes into a movie. Most amateurs try and cut a long form (over 10 minutes) movie in a single timeline. Professional editors organize each sequence in their own timeline (notice that Premiere Pro calles timelines Sequence 01, Sequence 02 etc.) and then combine those sequences into Scenes or a movie by combining the sequences into the final movie in a single timeline. In the end, this is a more efficient way of working on any project involving more than just a few shots.
Photoshop may be used to work on shots, but it is entirely unsuited as an editing tool. Photoshop and Illustrator are primarilly used to create elements like graphics or backgrounds that are used in After Effects or Premiere as part of the story.
The best workflow is the one that carries you to project completion with the fewest number of steps in the least amount of time. In nearly every case this means that you trim your shots into sequences in your NLE. The next step is to modify shots or sequences in a compositing program like After Effects. If you are working on individual shots in After Effects, it is almost always a good idea to give them handles. I handle is a few extra frames at the beginning and end to allow for fine tuning the edit in your NLE. Good rule of thumb is to add 30 to 60 frames.
Let's talk now, just for a second, about rendering. You are a little misinformed about rendering.
There are two types of codecs used to in production. The first is a production codec. This would be something like ProRez, or Animation, or even JPEG 2000, at the highest quality settings. To be classified as a production codec the rendered files must be lossless, or nearly lossless. Production codecs take up a lot of DriveSpace. Some of them will not even play back in real-time on any system. Many production houses use image sequences as their standard production format. You can render, remember, and then render again from into production codecs with no loss in quality. All you need is enough storage space to hold the files. Every production codec that I use is at least 10 bit color depth.
The second type of codek is called a delivery codec. These are highly compressed, playback in real time on inexpensive systems, and should never, I repeat never be used in the production pipeline. Anything in the MPEG class of codecs is a delivery codec and should not be used in the production pipeline.
Come to think of it, there is a third type of video codec. These are acquisition codecs. They are the codecs used by the various camera manufactures to record video. AVCHD, is a very low data rate codec used by consumer cameras. Other cameras from the consumer level to the pro level may use various forms of MPEG encoding. These "acquisition codecs" are not suitable for use downstream in the production pipeline at all. What I mean by that is, you should never render some original footage back to the original acquisition codec. The only exception to this rule are professional cameras and recording systems that record in lossless or raw formats right from the start.
One last thing. Don't forget sound. Professional polished productions always use specific sound editing programs to complete the audio track. While you can do a fair job in most NLE's, you can do a much better job in something like Adobe Audition. Cutting, editing, or adjusting sound and AE should be limited to reference audio or scratch tracks only. After eEffects will do a good job of rendering a lossless audio track from a clean original, but it's one of the most cumbersome and ineffective audio editing tools ever designed. Oh wait, AE is not an audio editing tool, so it's okay with me.
I hope this helps you along your path.