The PureCM Eclipse Plugin supports two forms of submit: 'Project Submit' and 'Workspace Submit'. 'Project Submit' will only allow you to submit files contained within the active Eclipse project. We imagine this will be the most common way of submitting your changes, so you are not confusing the changes you are making in one project with the changes you are making in another. 'Workspace Submit' will allow you to submit all changes within the PureCM workspace for which the active project belongs. This will allow you to perform cross-project submits if required.
To submit your changes to the server right-click the project in the 'Explorer' and select 'Team | Submit Project Changes to Server' or 'Team | Submit Workspace Changes to Server'.
This will then launch a modal dialog showing all the files available for submit.
If there are some files you do not want to submit you can uncheck them by clicking the checkbox. You must provide a description of the changes before you submit. After providing a description you can click 'OK' to submit your changes to the server. If the submit was successful then a changeset will have been created for the stream, and other developers can share your changes by updating their workspace.