If you are using your existing Windows users as ES users, you will probably want to set some of the new MSS-specific user attributes for at least some of them. For example, the microfocus-MFDS-User-MTO-Timeout attribute sets the MSS timeout for that user. See the ES/MSS documentation for more information.
You will also probably want to add existing users to MFDS and MSS user groups to reflect their roles (developers, administrators, etc). Note these are ES user groups, not Windows user groups, so you change them by modifying your AD repository with an LDIF file or a tool such as ADSIEdit. The ES/MSS documentation includes information on ES user groups. For example, you can add Windows users to the #DSAdmin group in Enterprise Server User Groups to make them MFDS administrators; to give a user permission to start and stop ES regions, set their default group attribute microfocus-MFDS-User-DefaultGroup to SYSADM.
You can make these changes manually using a tool for administering AD data, such as ADSIEdit. For bulk changes, though, you will probably want to create LDIF files to update multiple users, groups, or resources at once.