No problem.
What you are doing is just checking if the function exists and if it does, then inserting the suckerfish(); code and if not you continue to the next instruction.
So … it goes in the same place as your original suckerfish(); code was – normally the header.php file.
The functions.php file in your theme is where any functions which your theme uses are stored. So you definitely don’t need to put it there.
In the following example, the menu will display, but if the plugin is not installed, the text “Helloâ€