If I get the NF PvP edition

Do i get to use the hero system?

Presuming that you mean 'If I buy the Nightfall PvP unlock pack, do my heroes get access to those skills?' the answer is yes, as they are unlocked skills and heroes can use all unlocked skills. (Sorry if this comes out patronising or makes me looks like a jerk =P)

For your PvP characters, yes. However, since PvE heroes are unlocked per character by quests, you couldn't use them in PvE.

I am not sure if we are on the same wavelength here but I am referring to this,

As you advance through the game's storyline, you'll have opportunities to recruit adventurers (controlled by other players) and henchmen (computer-controlled allies). These alliances are temporary, usually long enough for you to finish a few quests or missions. The story also includes opportunities to recruit long-term allies: heroic non-player characters who play an ongoing role in the story. Completing specific quests allows you to recruit these unique heroic NPCs, commonly known as Heroes.

FYI, I only have prophecies.

Yes, if you buy the nightfall PvP edition, your PvP characters gain access to the heroes and the Nightfall skills, simple as that

So I do get to use the hero system, thanks!

indeed you do, but ONLY with PvP characters