Basically whenever the trinket procs, you are going to want to prioritize AM. So even if you are mid burn with arcane power up, instead of spamming arcane blasts you will want to do whatever you can to get as many Arcane missiles into that mark of doom. For your burn rotation you have 2 options. The first option is more safe and consistent.
1. you will get to 4 arcane charges regardless of when mark of doom is applied, then spam all of your arcane missiles and while the missiles are in the are drop your crystal and use arcane power and continue your burn rotation while using any AM procs into