Submitting whole chloroplast genome sequences could be a complicated task because of all the files and their formats required by GenBank. I have documented all the steps necessary to complete this task in a bitbucket repository:

https://bitbucket.org/oscarvargash/lecythidaceae_plastomes/src/master/genbank_submission/

Please consider citing the paper: doi:10.1002/aps3.1151

Good luck with your submissions!