In order to check in a file, the status must be "Logged Out". Then, using the square checkbox, select the files you would like to check in; this can be one or multiple files. Then, from the custom function menu option select the "Check In" option.
An image of the custom function menu.Once the custom function has been selected a message box will appear with the number of files being checked in written on it. If the number is correct, press the orange "Check In" button. If the number isn't correct press the "Cancel" button and check the files that have been selected.