Regarding the second question:
You control the [mwcard=DNJ01]Altar of Skulls[/mwcard]. So, here's a rules recap:
1a. You decide the order of events affecting your objects. So when an enemy corporeal creature is destroyed, if there is another triggered ability that affects a object you control (like [mwcard=DNJ04]Graveyard[/mwcard]) you decide which event you want to happen first, and therefore whether you place the skull token first or second.
1b. If the destruction of that enemy corporeal creature also affects objects your opponent controls, your opponent determines the order of that effect *only* in comparison to other events whose order she controls. She may choose any of her events to occur next, but may only choose from the events she is entitled to control (because those events affect her own objects).
1c. The player with initiative chooses the order of events when there is a conflict. So you decide the first thing you want to happen to your stuff, your opponent chooses what she wants to happen to her stuff, and because you have both chosen for something to happen, the player with initiative chooses one to happen. This technically occurs whenever both players have upkeep phase event they want/need to resolve, but only matters if those events can interact in some way.
1d. This process repeats for as long as there is a conflict. The player with initiative keeps choosing again and again between conflicting events until there are no further conflicts. This likely means that the player with initiative keeps choosing until one player or the other runs out of objects that need to be affected.
1e. If a single event affects objects controlled by both you and your opponent (e.g. transfers damage from a creature you control to a creature they control) the player with initiative chooses when that happens, as if it were an event that affected only his or her object.
1f. It's important to remember that neither player is required to declare an ordered list at the beginning of the upkeep phase. Both players are choosing events to occur *as they occur*, and the order in which those events happen becomes the order chosen. This means that players are free to change their minds about what they want to happen next depending on die rolls or choices made by other players.
1g. The is no specific rule that explains a procedure for revealing your choice. It's never mattered to me, but if it were important and I needed to make a rule, I'd suggest that the player with initiative may declare what his or her choice is last, after any opponents.
2a. So, back to [mwcard=DNJ01]Altar of Skulls[/mwcard]. Altar has a rule that is enforced "while altar has 8 or more skull tokens". This text isn't an if/then ability, so it's just a part of the game rules, not an event on its own and so not subject to having its order decided by anyone. It's either true or false, but no one decides when it happens. It's a consequence of the altar having 8 skulls, and it affects all creatures, but it is not a triggered event caused by putting the eighth skull on. You don't put the 8th skull on and then later give objects the effects caused by having 8 skulls.
2b. This is important because it means that the controllers of each and every living creature do not decide an order to give all those creatures finite life, one at a time. It happens all at once as a single consequence of the eighth skull event. If the 8th creature dies during the Upkeep phase, applying the 8th skull is a triggered event that is put in order by the Altar's player, and the Lifebond and Finite Life traits are applied as part of that event.
3a. Unlike its Finite Life ability, the final clause on [mwcard=DNJ01]Altar of Skulls[/mwcard] says, "[...] during the upkeep phase, each living creature receives 2 direct poison damage." This is handled similarly to what would happen if there were many creatures with burn markers: this will be many separate events, one for each living creature. The order in which a player's creatures are affected is determined by that player, and in the event of conflict, the player with initiative chooses the order, as previously described.
3b. Remember that both players are choosing an event to occur from among those that affect their own objects, and then the player with initiative is choosing between the conflicting options. As long as there is a conflict, the player with initiative may repeatedly select the option provided by the opponent, ignoring her own events for as long as possible, but the order in which those the opponent's events are offered up for approval is the opponent's choice.
3c. Also remember that events that affect multiple players' objects are chosen as if they affected the objects of the player with initiative.
4a. Sometimes events that occur during the upkeep phase cause new events that will also occur during the upkeep phase.There is no rule requiring these new events to wait until all old events have happened. An event is an event, and all events are candidates for every choice that a player may make in the upkeep phase.
4b. So, if Altar of Skulls is killing multiple creatures, and it matters which is the first to die because that determines how much mana is put on Graveyard, we follow the rules above.
4c. What is likely to happen in practice depends on which player has Initiative. If you have initiative, and you have a high level creature that may die this upkeep (by burn, Altar, Curse, Force Crush, failure to pay Upkeep +X, etc.), you may choose to kill it before ever allowing one of your opponent's choices that would kill a creature she controls. If you do not have such a creature, your opponent will likely not do you any favors, and will chose to kill her smallest creature first.
4d. If your opponent has Initiative, she will likely never chose to kill a high level creature before the lowest creature she has access to. If she can kill her own Fox she'll likely do that. You can prioritize the deaths of your own higher level creatures over your lower level creatures, but she can put any of her creature deaths before yours, and in any order she chooses. She's free to apply any-and-all of her events before ever allowing one of yours.
EDITS -- cleaned up the grammar a little, now that I'm at a keyboard. Typing on glass is tricky. :)
