That is up to you. You will always treat them in a separate container from whatever they are currently in. If you want your main reef to be SPS-free for 6 weeks, then your corals will need to be in a holding tank for the duration and each coral is treated in a bucket like you just posted.
In my case, I treated the affected corals and placed them back in my reef. My method isn't a guarantee of erradicating them from the system though, but I wasn't interested in setting up a full-blown secondary reef for the quarantine period.