Render is a weird and overused word.
In this case we are talking about "preview" render. In other words, the computer needs to work on your clip for you to see it play smoothly while you work on it. If you put enough transitions, effects or adjustments on the clip the computer and PrE may not get it perfect.
The green line means your computer has "rendered" or processed the clip for the smoothest play back possible. The yellow line means that the computer may need to process the clip and it's adjustments. In previous versions it was red instead of yellow. I don't think it will ever display red in PrE11.
To make the yellow lines turn green, press the Enter button and wait while it does the work. There is also a mouse clickable button on the same line and to the right of the playback controls.
With a project as large as yours, it may take a longwhile to do the whole thing. The Workarea Bars can be set to force the render to small sections instead of doing the whole project.
Even with jerky playback on a clip complicated by transitions, adjustements and effects the output may be fine. That's because at output everthing is "rendered" again to match the output product choices. It can take much longer to create the final product than watch it. If you are worried about jerky preview making it's way to the final output, try test outputs. Use the Workarea Bars to isolate the clip, pick the output you plan on using, check the box that says "Share WorkArea Bar Only" and see what you get.
Some comments as per whsprague with some additional observations.
You are addressing a Preview matter. When you first import your video into Premiere Elements 11 with the correct project preset for at video clip, there should be no colored line over the Timeline content (Expert view). That is the program's indication that it is giving you the best possible preview for what you are seeing in the Edit Mode Monitor. But, once you go to edit that content, you will see an "orange" line over that edited content. That is the program telling you that, in order to get the best possible preview for what you are seeing in the Edit Mode Monitor, you must Render the Timeline content. In Premiere Elements 11, there are several ways to do that:
a. Press the Enter Key of the computer main keyboard and wait for the rendering to complete as indicated by the orange line turning green. (Thereafter you deal only with an orange/green indicator system - no more no colored line/orange indicator system for that particular clip.)
b. Timeline Menu/Render Work Area
c. Click on the Render button at the top right of the Timeline.
Keep in mind if you have a state where
a. no colored line
b. green line over Timeline content
The program is telling you by that indicator system that it is giving you the best possible preview. And, if you use any of the means to inititate Rendering of the Timeline, you will get playback of the Timeline content in the monitor rather than the Rendering process.
As mentioned, when the indicators point to Timeline Rendering, you do not have to Render the whole Timeline. You can do so selectively by setting the gray tabs of the Work Area Bar to span just the area of the Timeline that has the orange line over its content.
You do not have to Render the Timeline at all, but it your windows of opportunity to catch a problem sooner than later. Still the best judge of quality comes by viewing the export on your player.
Also keep in mind, that each time the Timeline content is rendered, the program is automatically generating previews files which can pile up and eat up valuable hard drive space. So, the setting up of the Scratch Disks is of major importance as part of the Premiere Elements experience.
Also there may be times when you save/close a project with a Rendered Timeline (green line over Timeline content) only to open it a find an orange line over that content with all its implications. That is a known happening and another story. Best Render again selectively or as indicated.
When all is said and done, if the jerky playback problems persist even for Rendered content, then best to do a mini look at of the export to decide what next, which could include the usual computer maintenance and optimization, Premiere Elements settings, properties of the source media, and such questions and answers.
As a point of general information, versions earlier than Premiere Elements 11 Windows had a no colored line/red/green indicator system as compared to Premiere Elements 11 Windows with its no colored line/orange/green indicator system. (I checked, this is not a matter of monitor color calibration differences.)
Jerky or slow playback http://forums.adobe.com/thread/1071217
>high performance PC with windows 7, 64 bit, dual core proc etc
"High performance" and "dual core" do not belong in the same sentence
This message has a really good graphic about requirements - http://forums.adobe.com/thread/810750
With Win7 64bit, are you using the 64bit version of PE11, and how much RAM do you have?
How many and what size hard drives, and do you have your video files on a 2nd, separate 7200 RPM hard drive?
Never a partition http://forums.adobe.com/thread/650708 for more on partitions