1) What Exporter is to choose?
Cordova exporter.
I'm using the latest CoccoonJS Plugin available at Github
Just in case, use these ones: https://github.com/CocoonIO/atomic-plugins-c2
Cordova Plugins aren't supported then
They are <img src="{SMILIES_PATH}/icon_e_smile.gif" alt=":)" title="Smile">. Even on Canvas+: https://cocoon.io/doc/canvas_plus#supported-features
However, they must be adapted for Cordova 5.0.0
My Question: If I want to use Canvas+, then I only can add the plugins available at 'Cocoon' (at the Plugin tab on cocoon.io)?
No, you can add more plugins. You can use cranberrygame plugins in Canvas+ too.
My Question: How do I install the plugins correctly? And do I need to choose WebView or WebView+?
You can use the the plugins tab in the project configuration.
About the webview engine, it is up to you.
Here you have some information about Webview+: https://cocoon.io/doc/webview_plus
And here some about the System Webview: https://cocoon.io/doc/webview
Everytime I export and upload the files (built with Cordova) the settings at Cocoon.io will be overwritten. Even if I delete the config.xml file before uploading.
If you are sure you don't have a config.xml file inside the zip and you are saving the changes correctly at the cloud, please, send us the zip file to have a look at it, because it should not happen in the way you describe.