Quoted from Troz:
- No, the value is not collected when you hit a skull shot.
- Yes, the skull value directly relates to the value of each shot in chapters. Skull Value x Chapter Multiplier = Shot Value
- Hitting a skull shot will increase that skull's value.
Yes, you absolutely collect the skull value on each shot when you're not in a chapter. This is a completely valid and important strategy to build up a value pretty high then milk it during main (non-chapter) play. If you loop the upper loop at the start of the game, for example, you'll see 1000, 1025, 1050, etc. You collect the skull value for that movie and increase it. If you find yourself with a 36x shot and nowhere to use it, shoot for the highest valued skull.
The other main way you increase skull scoring is during chapters. Each SHOT has a skull increase value associated with it, and it increases more the harder the shot. Some examples: center shot +100, left orbit +200, left ramp +300, Tia Dalma +750. It behooves you to shoot harder shots first to get the benefit of the increase for the rest of the chapter.
You also get the increase associated with a character's shot if they're spotted, whether the spot is via Spot Character, because it's your chosen character, or a male/female spot from Angelica/Scrum. In some ways, this makes picking Tia Dalma even more attractive for her instant +750 any chapter she's in. Except of course your chapter multiplier increase is halved.
Finally, one of Henry's deals is he double-increases Skull values during chapters, so look out for that as well (so if you shoot Elizabeth during a chapter, the skull value is +600 after the shot).
Edit to add: Max skull score is 10K.