So...
Incubus shows up, Task Force X is activated, and neck bombs are placed. Flagg and June Moon infiltrate under the subway Incubus is at, and prepare a devastating bomb with a 2 second timer to take Incubus out. Enchantress is brought out, she leaves the bomb with Flagg and joins Incubus, who can heal her heart stab wounds inflicted by Amanda as Flagg (stopping the countdown at 1 second left) lets Amanda know Enchantress scrammed.
Flagg then leaves the bomb behind and leaves the city to pick up the rest of the Suicide Squad and Joker gets the guy who made the neck bombs. Flagg brings the Suicide Squad by helicopter to rescue Amanda; the plan, fly to Amanda's building rooftop, pick her up, and leave. They get shot down and survive, and walk their way to the building instead, taking out a few popsicles along the way.
The reach the building, find more popsicles in the vents and take them out. Diablo actually is useful at roasting more popsicles. They then reach Amanda, who takes out her own agents due to them not having clearance. Flagg shrugs, used to it. They escort Amanda to the roof without incident and other than a run-in with Joker (who simply wants to take Harley, and uses jamming signal by bomb maker to keep Amanda blowing up Harley) who picks up Harley and then takes off, they encounter no more popsicles or obstacles. Helicopter comes as planned and takes Amanda away, with the Suicide Squad's orders simply being to wait for the next helicopter for evac.
So literally, the reason why soldiers are escorting the guy who shoots good, the girl with a baseball bat, the guy who climbs good, the guy with boomerangs, crocodile man, and the guy with fire powers who doesn't want to kill... the reason they are sent with neck bombs is to escort Amanda from the top floor to the rooftop so she can then ride out in a helicopter.
No plan for stopping Enchantress was ever created by Amanda or the generals backing her. Good thing the big bomb was left under the subway, so that random soldier that was escorting the group could use it to blow up Incubus. All the random soldier even needed was crocodile man to keep underwater popsicles busy and someone to distract Incubus to be standing on a particular spot. As for Enchantress, she could have been stopped at any time by crushing her heart. Her superweapon just needed to be bombed.