Oh I see, I thought you were going to integrate just the 2 chicks groups before integrating both with flock. 3 x 6 with how many chicks?
How big in feet by feet are the coop and yard?
....and how many birds in the other chick group and the flock?
The older chick group may be especially aggressive due to being low birds with the flock.
It's all about territory and resources(space/food/water).
Existing birds will almost always attack new ones to defend their resources.
Understanding chicken behaviors is essential to integrating new birds into your flock.
Confine new birds within sight but physically segregated from older/existing birds for several weeks, so they can see and get used to each other but not physically interact.
In adjacent runs, spread scratch grains along the dividing mesh, best if mesh is just big enough for birds to stick their head thru, so they get used to eating together.
The more space, the better. Birds will peck to establish dominance, the pecked bird needs space to get away. As long as there's no copious blood drawn and/or new bird is not trapped/pinned down and beaten unmercilessly, let them work it out. Every time you interfere or remove new birds, they'll have to start the pecking order thing all over again.
Multiple feed/water stations. Dominance issues are most often carried out over sustenance, more stations lessens the frequency of that issue.
Especially pertinent: Places for the new birds to hide 'out of line of sight'(but not a dead end trap) and/or up and away from any bully birds. Roosts, pallets or boards leaned up against walls or up on concrete blocks, old chairs tables, branches, logs, stumps out in the run can really help. Lots of diversion and places to 'hide' instead of bare wide open run.
