To help organize your emails, you can create folders in the Inbox to separate emails that you want to save.  In Thunderbird this process couldn't be easier.  In your Thunderbird client, on the left side you will see your "Inbox" along with a few default folders such as Sent and Trash:

Right click on the "Inbox" and select "New Folder."  A new window will pop up asking for the name of the folder:

Put in the name you want for the folder, click "Create Folder," and now your new folder is ready to use!