Organize scenes when making movies in AE

Dynamic Link is an excellent way to pull a shot into After Effects so you can do the compositing and animation, but there are some limitations. As long as the AE comp is fairly simple and will render quickly, you can maintain an efficient workflow, but when things get complicated and render times go up, keeping the Dynamic Link live can cause real problems. Suppose the render time gets higher than about one frame per second. In that case, I always Render a production master (High Quality or High Quality With Alpha) video and replace it in Premiere Pro. I do that because rendering a Dynamic Link in Premiere Pro opens a background copy of After Effects on your system to render the file. Rendering is always slower. The likelihood that a complex project with GPU-accelerated effects will hang or fail is higher, and the Previews in Premiere Pro are always compromised when you try to preview Complex comps. 

Here's my standard workflow for moving a shot that will take a lot of resources into After Effects. First, I always change the label color and rename effects shots in the Premiere Pro timeline so they are a different color, duplicate the shot in the timeline, and stack the duplicate on top of the original to a track that is dedicated to effects shots, so I have a copy of the original shot in the timeline. I then select the labeled, renamed, and moved shot, and sometimes add a few frames to the head and tail of the shot as handles if there is a chance that I'll need to fine-tune a cut or transition by a few frames and create the Dynamic Link. If the shot is complex, I return to Premiere Pro and undo the Dynamic Link as soon as the new comp is created. I often create comps with a hundred or more elements that can take several seconds to render. I start redesigning the shot when render times approach three minutes a frame. When the shot is complete, I use the Render Queue, not the Media Encoder, to render the high-quality production master (10-bit or better). The render is imported into Premiere Pro and replaces the shot in the timeline. If I need to redo something later, the effects shots are easy to find in the Premiere Pro timeline, the original footage is still there, and the workflow is efficient. 

So yes, I use Dynamic Link all the time, but for my projects, because of the complexity of the shots, I almost always Render the shots in After Effects/Render Queue instead of keeping Dynamic Link active. Here's a flowchart of a recent project that will give you an idea of how complex those projects can become:

The first column shows 16 shots from the first act of a 6-act feature I worked on with relatively simple comps that took a long time to create. Leaving all that work to render In Premiere Pro using Dynamic Link would have slowed the process and been much less efficient. That flow chart represents about three weeks of work on that project. It would have been a bad idea to keep all those shots as active Dynamic Linked comps. 

So yes, Dynamic Link is a good way to link a shot in Premiere Pro to a comp in After Effects, and as long as the comp is simple and will render quickly, you can keep it live and work efficiently. On the other hand, when render times start climbing, you will save time in the long run by rendering the AE comp in After Effects and replacing the DL Clip in Premiere Pro with the rendered clip. Dynamically linked comps in Premiere Pro always take longer to render than in the Render Queue. Sometimes four or five times longer. It all depends on the complexity of the comp. If all you are looking at is render time, rendering your effects in After Effects is always going to save time.