It should be noted the canton 9k have two sets of speaker terminals one set for medium and high frequencies and another set for bassThat is for Bi-amp/Bi-wire, nothing to do with subwoofer connection.
Given the above which is the best method (for musical benefits) to connect the sub or does it even matter which of the two options I use given my system?It is system dependent, my suggestion is try both way and let your ears decide, what sounded best is the best method.
If you can't hear any difference, I suggest go for line level connection, I think your integrated amp has the option of remote turn off the pre-out, which is good for late night listening.
Is one method safer to use than the other?IMO, line level connection is safer, you have less chance to shorted the speaker cable.