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Say a squad of Banshees with an Exarch led by a Farseer charges a squad of Tactical marines with a sargeant armed with a power sword led by a Chaplain, in cover. So we got 2 squads with a total of 4 characters here.

Since the Eldar player is the charger, he declares challenges the following way: the Farseer issues a challenge to the space marine sergeant and the Howling Banshee Exarch issues a challenge to the Chaplain.

The Space Marine player accepts both times, since he doesnt want any of his guys to miss out on attacks.

Ideally though, the Space Marine player wants the Chaplain (who has a power maul with only AP4) to be engaged with the Farseer (so his S6 Crozius Arcanum attacks can cause insta-kill), and his sergeant to be engaged with the Howling banshee Exarch (as he has the potential chance to survive the Exarch's attacks if she rolls badly and then strike back with the Power Sword and kill her)

How will the space marine player do this on the next turn using Glorious Intervention?

You can only have one ongoing challenge per combat. Also you don't get to pick who you challenge, you declare the challenge with one of your character and you opponent picks who responds.

Your scenario is not legal ('Issuing a Challenge', first sentence in bold).

good. now I can put that confusing thought process aside