Personally when I feed live rodents, I always use tongs to grab them by the scruff. That way when I present it to the snake it is much more likely to grab the rodent by the head and therefore less likely to be bitten.

With mice I sometimes use the tail, but rats are much too heavy to be held by their tails so you're best off with the scruff (I've heard of their tails actually coming off, not my cup of tea)