Dataset and users access in Enterprise edition

Where do you keep mapping between datasets/folders and users access( query or edit permission) in enterprise edition.
The permission set at top level is not getting applied automatically on nested folders/datasets

Settings on the space/folder are not applied to existing datasets. They are applied to new datasets going forward.

For existing datasets, you set permissions on each dataset.

Does this answer your question?

Is this information accessible to us ? through Rest API or query ?

They will be available via REST in our 2.1 reeleaae, due out in the next few weeks.