i'm never sure with this initiative thing: during upkeep the controler of the object affected chooses when it happens... but there can be simultaneousity problems...
I'm not sure if simultaneousity is a word, but I like it and will roll with it. This is definitely a major issue with the timing rules. Not because of how it's handled, but because so many effects are interpreted as being simultaneous when they're not. Mage Wars actually HATES simultaneous effects, and they're almost nonexistent within the game. Pretty much any time two things TRY to happen simultaneously, the game says to handle them individually one at a time regardless of what they're trying to do.
So, any time you think things would happen simultaneously, try seeing if there's a way to resolve them individually and if there is, that's probably the correct answer. With Malacoda, resolve each application of damage as a separate individual effect, with the timing of each determined by the controller of the creature being damaged. Like others already said.
Usually, the only time things are required by the game to happen simultaneously, is when something is being transferred. The notorious example is Death Link transferring damage from one creature to another, which requires the healing and damage dealt to occur simultaneously. There may be other instances of effects having to be resolved simultaneously besides transferences, but I can't think of any right now. But 99% of the time when something seems like it would be simultaneous, that's not how it is treated.