Preparing maps for offline use in Collector for ArcGIS for the first time can be a daunting process. However, Esri provides thorough documentation here.
You may encounter issues with downloading offline areas if you refer to the same layer twice in your service. In the Prepare data for offline use documentation, it is stated that, “A feature service published to ArcGIS Server or Portal for ArcGIS that contains two layers based on the same feature class cannot be taken offline, edited, and synchronized. For example, if you add your roads feature class to your map to display all roads, add the same roads feature class and set a definition query on it to display roads that are under construction, and publish a feature service from the map, you cannot take the feature service offline for editing and synchronize your changes when you are online.”
Although there is an enhancement (ENH-000126753) logged for this issue, the recommended workaround would be to create Hosted Feature Layer Views. However, if you would like to utilize services from your own ArcGIS Server, you can publish separate services for these layers.
For reference, here are the slides from today’s AGOL User Group Meeting Trash Monitoring Program (TMP) Collector for ArcGIS App demo: Trash Monitoring Program Presentation Slides
Thanks!