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That depends on how your pool is plumbed. If you have normal returns, in addition to the in-floor cleaner, it should be possible to use only the normal returns, and not send any water to the in-floor system. You may already have valves that can make this switch, or you may need to do some plumbing.
If you do not have normal returns, things are more complex. With many brands of popups it is possible to remove the popup portion of the fitting, allowing water to come out without anything popping up, but that is not always possible.