What does the database symbol mean in Eclipse icons?
I marked the database symbol in two places here:
it depicts the project is version controlled. And the file has not been modified locally since your last check out. & the number is the version number. The file without the number is newly added, i.e. not version controlled.
to check in to TFS:
right click on the project (not just a file)
select team
select check in pending changes
now you'll get a window showing files with changes (including new files), you can select whatever you want to check in.