Choosing to monitor multiple domains in one app versus a single domain app has pros and cons.
With one app per domain, you ensure that the data collection across domains is evenly distributed, or distributed according to your choice and not randomly. You also benefit from less potential impact from per-app system limits. For example, we have a limit on the total number of unique page URLs collected per app, so by splitting across multiple apps, you have more headroom.
However, you might want multiple domains in one app in order to have the reporting for the multiple domains more tightly integrated. Currently, we do not have the ability for charting multiple apps together, althoughwe are planning to support it in the future. The solution now involves making dashboard widgets for each app and combining them in a single dashboard.