When I start a new sketch, I only get the sketch project and not the one for the Arduino library. What am I not doing? Running jantje's V2.2 with Arduino IDE 1.2.6-r2 on my Windows 7 PC.
That is the main difference from a user point of view between V1 and V2 of the plugin. In V2 there is no longer a arduino project but you have a arduino folder in your project. This is necessary to support the menu structure but was initially created for the teensy.
This noob, too, is having problems uploading to my Yun from eclipse.
I'm using eclipse and yun on a weekly basis and I do not have any problems for uploading. I even modified my own openwrt solution to be compatible with the yun upload process and that works fine to.
Basically if you can upload with the Arduino IDE and you have some basic eclipse skills you should be able to upload with the eclipse plugin.
If you want more support you will need to describe the problem in detail. FI give a screenshot of the arduino project properties and the content of the upload monitor.
PS As you state you are a noob: Are you aware the upload does not compile the project? So you need to compile before you can upload.