I pretty much did what Gremxula said, probably initially at his suggestion. He knows what he's talking about. As for my answers...
1: The directions in Gremxula's Growth Map readme really can also be used as instructions to make your creature self-sufficient, you just have to teach him to only sleep when exhausted after you're done or he'll be useless at night. After that, only interact with him when he is either dying or doing something you don't want him to do (spank him), and if you really need him to perform a specific task. For me, controlling the creature and fighting alongside it is half the fun, but I managed, over ~100 in-game years, to get a creature that could also function self-sufficiently and win a skirmish by itself about half the time (admittedly sometimes I'd come back to find it dying repeatedly due to being zapped by the enemy). To be perfectly honest, starting a new game now, I marvel at how I ever trained any creature in the first place. As Sable says, they are "slightly headstrong," clearly an euphemism for "willful bastards."
2: As Grem said, fish. There is an infinite supply of it, and in most maps and all of the storyline maps, there is plenty of it all around. Just make sure you have the patched version or it will make him evil. I'm not sure if it's actually true, as I have not tested, but apparently eating meat makes your creature stonger. But meat is not really very renewable, as animals breed slowly. If it's fish, it's unlimited, and a fat creature can take more hits, has more endurance, and can cast more miracles, all of which are also traits that you want to accent in the slow-moving, tough and intelligent turtle, whereas a skinny creature has a large bonus in speed and thus is better in pure combat. If you have a tiger, wolf or leopard, skinny is the way to go, which is harder to do, but for the turtle and bears in particular you'll want them fat.
3: When he reaches 50-100% tiredness the first time you interact with him after the growth map, make him sleep and when he wakes up pet him to 100% (make sure that it isn't night time, or he may think you are petting him for sleeping at night, a habit you should have already broken him of). The next few times he gets that tired and sleeps, pet him to ~90% or 80%, to make sure he doesn't get inot the habit of only sleeping when he's slightly tired and never sleeping when he's very tired, or eating when he's a little hungry but very tired. Then, when he reaches 30%-50% tiredness, pet him to 70%, and the next few times pet him to 60% or 50%. When he sleeps at 10-30%, pet him to 40%, and the next few times he sleep in that range pet him to 20 or 30%. Then, when he sleeps at ten percent or below, reward him to ten percent. That should teach him to sleep in correct proportion to his tiredness. Note that you may have to repeat much later in his life, when he will start acting weird.
4: Any time after he's fully grown, teach him whatever you have the patience for. The first four miracles he learns will likely be his favourite unless you take special measures to fix it, so I suggest food, wood, heal and one other, perhaps birds, for a good creature. A word of advice: If your creature is good and you plan on using him to megablast temples, megablast should probably be the only offensive miracle you teach him, unless you are very patient.
5: I use Kilroy's for training, actually. It's just the easiest, even if you have to drag the miracles about to teach the creature proper usage, and it can also be used as a sort of a "rest house" to feed, rest and exercise your creature in the middle of the story.
