You cannot assign characters to keyboards in FontCreator. You can only map characters to code-points. Capital Y is code-point 89 (decimal) or 059 (hexadecimal). Lowercase y is code-point 121 (decimal) while lowercase ÿ umlaut is code-point 255.
Deciding how to type a given character (code-point) with the keyboard is not a FontCreator topic, which is why I moved your first thread to this General Font Discussion forum rather than to the FontCreator support forum.
Lowercase ÿ can be typed by holding down the Alt key and typing 255 on the Numeric keypad. This method can be used for many other characters too, but its not very user-friendly. So, before designing your font, you need to give a great deal of careful thought to how users are going to type with it. If they need to install custom keyboards or customise their word-processor, that is a barrier to your font being popular. For a Devanagari font, I suggest designing it to work with the standard Windows Devanagari keyboard. I am not familiar with using that keyboard or typing Devanagari.
In Word-processors like Word or OpenOffice you can map characters to keyboards using the modifier keys, or the Microsoft Keyboard Layout Creator will let you map characters for use with all installed programs, even those like Notepad that don’t support keyboard customisation.