Two card ships confuse me, and more so with modifications.
For the sake of example here let's assume I am only talking about an imperial raider, and when I ask a question please fill in the "well I was told and we thought" on your own 
When firing a primary weapon, why can I only use the front arc?
Why does the new ordinance tube upgrade affect both halves if secondary weapons don't?
Can I put a modification on both the aft and the fore section?
> When firing a primary weapon, why can I only use the front arc?
Because only the fore card has a weapon value printed on it. Also because an email from the game designers said so. There was already a 20+ page thread about this before (I take the blame for starting it) that came to a crashing halt when the email showed up.
> Why does the new ordinance tube upgrade affect both halves if secondary weapons don't?
I believe it is because modifications are attached to the ship as a whole, not any one ship card. There may even be a specific FAQ ruling about it, and if there isn't, expect one to show up eventually. Secondary weapons don't because they're specifically attached to one ship card.
> Can I put a modification on both the aft and the fore section?
No, because the limit is still one modification per ship. The Raider is still just one ship, even though it has two ship cards.
And for further information, you can't go past this:
> Why does the new ordinance tube upgrade affect both halves if secondary weapons don't?
I believe it is because modifications are attached to the ship as a whole, not any one ship card. There may even be a specific FAQ ruling about it, and if there isn't, expect one to show up eventually. Secondary weapons don't because they're specifically attached to one ship card.
Modifications should actually be attached to one section or the other. It will have the same effect on the ship regardless of where you attach it, but it is important for scoring a ship with a crippled section.
Secondary weapon upgrades don't affect both sections of a ship because the rules say they don't, to put it simply. In general, upgrades on a two-card ship will affect both sections, but the rules lay out two exceptions:
1) Secondary weapons use the arc(s) of their equipped section
2) Upgrades with the "Action:" header can only be used as their equipped section's action