While everything that discens said is correct, one thing bears explicit mention: there is no change to the level of granularity of Team Foundation Server. You still check out files and edit files and check-in files.
In your example, if you have a file checked out and you edit it in Notepad, the changes will be checked in. There is no change here from previous behaviors. There is no way to keep these changes from being checked in, short of saving the file with a different file name.