To my understanding.
The mercenary box set is what allows you to create your own mercenary force with your players as the leadership in the game. That along with the small campaign on how to use them and the costs to keep one operating. If you wanted to be a more military themed Traveller Campaign instead of a trading campaign that leads to combat.
While Mercenaries of Charted Space talks about more famous mercenary teams in various places of charted space. Where to find markets to hire mercenary teams, along with some potential places that mercenaries might be used as active conflicts.
Both them were written before the 5th Interstellar War books. So take some of the information that is presented could be considered "out of date" because of the war now.
I would think they are completely separate information, but could compliment each other. As a GM with both, you could set up that your PCs create a merc team. Then are in a market looking to broker their services, finally arrive into a region and maybe facing off against another merc team.