Well, first of all it may help if you've got a high luck or magic stat (preferably both, though the luck stat may have more effect on your attempts) on the character that's attempting to manipulate the serpent.
Second, I THINK there may be a relationship between how much of the creature's HP is left and the success of the "Manip." command, meaning that you may have to "weaken" the creature with a few hits first before trying to manipulate it.
I haven't played that section of FF7 in a LONG while, however I've noticed that there is definitely a type of connection between special battle commands (like the "Card" command) and HP in FF8, so maybe the same thing is going on here.