So after playing a few times and reading the rules, I'm still unclear on ship-to-squadron combat.

Take for example a Victory Star Destroyer that you get in the core set. Regardless of which version you use, say there are enemy squadrons in the rear firing arc zone (the number of squadrons doesn't matter). Anti-squadron rules say the VSD can use one blue die, however, its rear armament is two red dice. Does this mean you cannot attack fighters from the rear zone or do the red dice only apply to ships and the blue dice can be from any zone?

Anti-Squadron armament applies to all hull zones and is completely separate from ship attack dice. A VSD then can attack every squadron in a given hull zone with one blue die as it's attack. Hope that answers the question.

Your anti squadron dice is used from any arc, the dice you use to shoot at other ships do not factor in your antisquadron dice. You can shoot at all squadrons located in that arc that you are firing from.

Since ISDs have 2 blue dice they will use 2 blue dice to shoot at medium range for their anti-squadron dice, from which ever arc you choose.

if you have a ship with one blue and one black then you can use the one blue at medium range but the black and blue to shoot at squadrons from short range, even though they are in the same arc. Each attack is deemed a separate attack within that arc until all squadrons have been shot at.

Like modise said, it's 2 different things. The dice featured on the arcs are only for anti-ship. The anti-squadron dice can be used from any hull zone as long as you've got range. And it's going to target every squadron in range (with each squadron counted as a different attack for card effect purposes).

To add...

@Nethus- Your ship has different Hull Zones, and those Hull Zones have both Battery Dice (versus Ships) and Anti-Squadron dice (versus, guess?),

A ship can fire twice a turn but they each must be out of a different Hull Zone. When firing out of a Hull Zone you must decide what your target/s will be. THAT will determine what dice are used.

Battery weapons fire at a single Ship.

Anti-Squadron weapons fire at all enemy squadrons within the arc and range of the firing Hull Zone.

So, each Hull Zone has both Battery and AA. You may fire out of two zones. You cannot fire out of the same Hull Zone twice (without upgrades). Target type determines what dice pool is rolled.

and don't forget that its one or two blue die rolled on each stand of fighters in a ships hull zone target area.

That clears it up for me. Thanks so much, everybody! Can't wait to see what Wave 3 brings us!