I would apply the skeleton template first, then the advanced. The reason for this is that the skeleton template sets the charisma for the creature to a specific value and the advanced template adds 4 to all ability scores. If you were to apply advanced first, you would lose the increased 2 HP per HD from the advanced template.
Also, it depends on the purpose you're going for. If this is to design a monster and you want to use the CR adjustment for those templates to tailor your encounter then apply as I described above. However, if this is coming up in play where someone is casting animate dead on a corpse of an advanced giant gecko, then apply the skeleton template second, on top of the base creature (advanced giant gecko).