Who Are The Six Seas?
The Six Seas are six men and women who're given free reign to keep those under the thumb of the Triad in-line. In the time of the film, the South-East Triad hold 80% of the drug and weapons trafficking trade, and the Six Seas are the specially chosen and most dangerous enforcers they have to keep such an expansive empire in check. Their methods are merciless and their objectives are often part of setting an example; only a few inhabitants of the village Ito was sent to kill were acting against the Triad, but that didn't matter.
Becoming a Six Seas means working your way up the ladder of trust within the Triad, until, as the proposal Arian received highlights, either an active member dies or betrays the cause and requires taking out.
In the spirit of John Wick, the film approaches organized crime with a layered mythology. Alma and Elena are regarded as numbered Lotuses, third and fifth respectively. They serve Chien Wu, one of the Six Seas' beck and all, doing the dirty work so he doesn't have to. The implication is that the Lotuses are another elite group, perhaps more removed from the Triad, who occasionally work in tandem with the Six Seas.
Who Is The Operator?
The Operator, played by Julie Estelle, is the most mysterious character in the film, having no backstory provided even by the time the movie ends. She appears in the parking lot during the first wave of attacks from Chien Wu, then tries to kill Ito in his apartment before his story convinces her to fight with him instead of against. She's the only one acting independently, having just heard there was a reward on Ito's head, with no explicit or implicit affiliation in her actions.
She represents the Triad not being as powerful as it thinks it is. Her power, resources and capabilities are incredible and very distinct to what the Triad has at hand. She has military-grade explosives, guns and other equipment, and a very strong supply of them, and her martial arts prowess is possibly the greatest among all the characters. She also identifies Alma and Elena, meaning she knows the systems she's working against here, possibly hinting that she was once part of it before somehow getting out. Either way, she is an invaluable asset to Ito and a not-so-implicit blessing to Reina.
Where Was Reina Going?
The boat Reina ends up on has no destination displayed. The movie takes place in Macua in Indonesia, so there are several possible places she could be headed – Philippines is likely, being easily accessible by boat, but there are other islands and countries in the vicinity too. What's important is that she got on the boat and is now effectively lost to those that were hunting her. By making sure she can have a new life, Ito's redemption arc is complete.
This whole thing was put in motion because Ito couldn't shoulder the kind of ruthlessness the Triad and the Six Seas require. No regrets, second thoughts or second chances. By saving her, he figured he would be doing some good that would put him on a path of righteousness after a life on the wrong side of the street. He knew he wasn't going to get out alive, and even though it hurt, his crew knew the risks of the life they were leading too. Reina had a chance to know a different way of existing, free from mob rule, and in freeing her, maybe - just maybe - his soul could be redeemed. The film doesn't give a definitive answer, but as she sails away Ito goes out fighting on the right side, and that definitely counts for something.