What exactly are you trying to accomplish or what do you mean?
Because when using Admin Backup/Transfer, the backups will include all domains. On the new server you can import everyting again with Admin Backup/Transfer. In that screen, you can define that you want to use the new nameservers.
So best is to first transfer only the admin account, then change nameservers, define the new ones. After that is done, go to Admin Backup/Transfer and setup the nameservers to be used on restore.
After that, restore resellers and after that customers.
That would be all.
If your new server has new ip's you do have to change the nameserver ip's with your registrar.