When an ElastiCube is created in the desktop version of ElastiCube manager, only a .ecube file gets created, whereas when an ElastiCube is created in the web version of ElastiCube manager, a folder with the ElastiCube name is created that contains few subfolders. The folder is created in the path C:\ProgramData\Sisense\PrismServer\ElastiCubeData.
Do the desktop version and web version of ElastiCube manager work differently? What do these folders hold? Is it a good practice to first create the ElastiCube in the web version of ElastiCube manager, so that the folder structure gets created and then use the desktop version for any modifications that cannot be done using the web version?
Both the desktop and web ElastiCube Managers create folders here C:\ProgramData\Sisense\PrismServer\ElastiCubeData after the first cube build (and subsequent builds).
The desktop version does this after the cube is built for the first time (and updates these folders each time a build is done).
When you open a cube from the Server Console on the desktop, you're really opening the .ecube file stored within C:\ProgramData\Sisense\PrismServer\ElastiCubeData\<cube name>
When you create a new cube and save off the cube, you're really saving the schema (the .ecube file) which contains the relationships between the data but doesn't actually store the data from the data sources. This is nice when you want to do some versioning of the schema (in case you need to change the data model, are testing some relationships, etc.).
The web version also creates a folder in C:\ProgramData\Sisense\PrismServer\ElastiCubeData on first build.
These folders in C:\ProgramData\Sisense\PrismServer\ElastiCubeData store the schema of the cube and all of the data (tables, views, etc.) that have been imported into the cube.
As for a recommendation for building cubes, keep in mind that the desktop version of ECM is more stable and has more features but the web ECM is easier to access (no need to get onto the server) and has greater sharing capabilities with select users.