You have the ability to configure, run and work with more than just one project. That's why you have two listings here.
Certain functions are not available when a project is running (searching, checking and/or submitting). Other than that, you can always right click on the project or website to open popup menus for more options.
There are different colors that should give you a quick overview:
An interesting feature that you might want to use is a manual submission to a website. You can right click on the website and choose “Submit Message” (preferable when there was already a check done). A form is shown and filled with the data that the program would normally input on a automated submission as seen below.
It of course makes sense to review things before you start a project and submit the message automatically.