What's Amanda Waller's game? She targeted the Secret Six with two apparent goals: To get Deadshot back on the Squad, and to lock the rest up (where they could be used by her at her convenience later, if necessary).
Then it turns out Waller is also Mockingbird, the person hiring the Six recently. Which means Waller (not Vandal Savage, as I theorized last fall) sent them to that prison island, and sent them to Belle Reve to be attacked by the Squad in the first place. When all was said and done, the Six weren't captured, Deadshot didn't rejoin the Squad, and Waller has a bullet too close to her heart to operate. Naturally, the Wall is not bothered by any of this.
OK, I understand her idea that now that Deadshot's made his feelings clear, he might be willing to hire back onto the Squad later. he shot her, and if Waller doesn't care, well then Floyd probably won't either. I also think I understand why she's unperturbed by the Six still running free. She can still use them (without them realizing it), and they fact they stood together against her may make them a more effective team. It's a massive, bloody, ridiculous team-building exercise.
There are still two questions I have left. One, why use the Six at all? She already has Task Force X, who she's more familiar with, has more people she trusts (assuming Waller trusts anyone), and more control over. The advantages of the Six are they only receive money, not time off jail sentences (no need to explain why so-and-so is already back on the streets), and there's an extra layer of deniability with the Six, since they could be working for anyone who'll cut them a check. Also, the Squad has a few people with scruples who might (I emphasize might) object to certain jobs (Bronze Tiger, Nightshade, maybe Rick Flag), which the Six likely will accept. So perhaps the Six are who Waller turns to when even her official hands are tied.
Second question then, why hire them for that prison job? It seems she would have to be involved somehow, since she hired them for Mr. Smyth, and he had no issues with the hire. If Waller expected them to protect the construction of the prison, she misread them. Which could happen. Amanda Waller does make mistakes. Or she was counting on the Six to dislike the job sufficiently to help bring the prison down. If that's the case, I can understand Waller sending the Six. Smyth mentioned all the Amazon prisoners were there with the express consent of the U.S. government, and Waller is too smart to openly cross them. Maybe locking every criminal in the world in that prison would cut down on her access to recruits for the Squad. Maybe she dislikes the idea of simply locking up all the world's criminals in one place. The potential for evil networking is remarkable. Or maybe she dislikes the idea of all the criminals being locked up in a place not directly under her control.
Is Checkmate still active? Waller was pretty high up the totem pole there as well, so she could be using the Six for Checkmate-related activities she either couldn't get the other honchos to sign off on, or for missions Checkmate approves of, but needs to be able to distance themselves from in the event things go wrong.