Hi, depending on the nature of your mitochondrial sequences, whether specific marker genes or whole genome, there are different submission routes.

If you have specific gene regions such as COI or D-loop there are pre-formatted annotation checklists available which facilitate data entry across multiple files of the same sequence type. Only the variable fields are filled out per sequence while static data can be propagated automatically. The process allows you to select only fields for which you have data for. Of those, you can flag which are variable and which are to remain static. There are also options to create custom spreadsheet files for the convenience of data input using your preferred software or alternatively import your FASTA file and using the metadata provided via the spreadsheet or interactively in the submission system, the INSDC feature table format will be created automatically.

Please check this for the currently available annotation checklists: http://www.ebi.ac.uk/ena/submit/annotation-checklists

If you have a complete mitochondrial genome you would need to create the feature table format yourself and then use an Entry Upload option. For more details please see: http://www.ebi.ac.uk/ena/submit/non-study-assembly-submission

The submission system for assembled and annotated sequences can be accessed via: https://www.ebi.ac.uk/embl/genomes/submission/app/login/login.jsf

You can write to ENA help desk at datasubs@ebi.ac.uk for assistance.