Hello Luo
1. On data extract - the best way to load incremental data is to use file upload. You can use MDMGX extractor to load the initial data and then use file upload for loading subsequent data.
2. If you make any changes directly in ECC, definitely it is for limited set of data. You can change the data in MDG manually with the proper approval process. Create a separate change request type to handle all such requests. Its better for tracking.
3. For loading reference data, you can use BC sets or do the direct table upload in MDG through transport. Attaching the list of all the tables. Create BC set and upload the reference data in MDG or ask basis team to transport the tables listed in the excel.
Kiran