When you check in a document, it is always checked into the branch to which you are currently connected. If you want to check your document into another branch, you must change branch before beginning your check in.
For more information about changing branch, see Changing branch.
When you have completed your check in, you can confirm that your document version has been added to the correct branch by opening the property sheet of the branch and clicking its Members tab (see Managing branch members).
For more information about checking documents into branches, including the various modes available, see Check in modes.