Nucleotide Sequence Submission System (NSSS) is an interactive application to enter all of items required for your submission on step by step basis.
To use Mass Submission System (MSS), submitters have to make submission files by themselves.
However, since NSSS can not accept all types of sequence data, it may be required to use MSS for your data submission.
Use Submission navigation.
See Workflow of the data submission to DDBJ
Based on above information, select either of them as needed.