Netro smart algorithms estimates the moisture level and add smart schedules if it will drop below the threshold. If you add manual runs, the moisture may be above the threshold, hens smart schedules will be cancelled. But new smart schedules will be added later. In short, Netro smart schedules try to keep your moisture level in a reasonable range. Netro updates smart schedules even without manual watering, e.g. if weather forecast data changes, your smart schedules will be updated as well.
I guess your real problem is that the default smart schedules can't provide enough water. If that's the case, you could try "boost" mode in setting->zones->smart zones->mode. You can also add programs in setting->program if you know how much water your yard need. Netro smart will skip the program if it's e.g. raining.