Hy Jeff,
as I know if I you develop a new embedded report based on data from entity store, or customized entity you should add the new report (pbix) as a resource to your deployable packages. We recommend not to change the original aggregated entities and reports, instead copy the aggragte entity classes and the pbix files and customize as you need. They should be part of your package you deploy. There is no need to deploy the reprorts via LCS, as embedded reports should automatically be deployed to Power BI embedded service the first time when they are called from User through GUI.
If you need data from other data sources as Dynamics 365FO (only direct query works) or you need to have the reports in PowerBI Servcie available to consume without Dynamics 365FO, then you can import these reports into LCS. Afterwards you have deploy the reports from inside your D365FO environement (UAT, Prod, ...) to Power BI Service using "System Administration/Setup/Deploy Power BI files". If you deploy this way the D365FO data source will be adopted to your current environement at the moment of the report deployment.
After this you can the consume the PowerBI Reports inside PowerBI Service (without Dynamics 365FO) and share within organization or individuals. This needs Power BI pro LIcenses as I know. Furthermore you can this deployed reports then integrate in D365FO using personalization (Options "Open report catalog", Open dashboard catalog" or "Open tile catalog", this works on most of work spaces). This way we can visualize data form outside Dynamics 365FO inside the application, e.g. Third Party data from Logistics or Production plant.
