For Vertigo, you more or less spam it at every opportunity against clusters or enemy units. Generally speaking, any enemy force that's worth using Vertigo on is a mortal threat to capital ships, so just use it as soon as the cooldown comes up on the biggest cluser of units within range while maneuvering the Rapture as best you can.
Keep in mind that Vertigo has an exponential increase in performance as it levels up. It's somewhat lackluster at level 1, excellent at level 2, and jaw-droppingly good at level 3. Getting your Rapture to level 5 is the trick to make it really shine.
As for magnetize, that's tougher to pull off. You need to get in close to activate it, and timing is an issue. Really, no right answer; try to use it when there are lots of strike craft (preferably bombers) overhead and/or you want to shut down the enemy's abilities.
The dunov is a BRAWLER. It goes in close with the rest of its fleet and it has amazing staying power with its shield restore
Except shield restore cannot self-target, and building multiple Dunovs will cut your firepower so dramatically that the enemy will be able to overwhelm your fleet easily. Personally I only use it in the TEC vs Advent matchup for EMP; too fragile to even consider when faced with typical LRM or Assailant swarms, but against Advent the ability to cut through both shields and antimatter in an area of effect is way too good to pass up.
