Discuss with your project supervisor?
Packetize the data and encrypt at the packet level.
I am working alone on it ... there is no manager or anyone else
Your question lacks much in the way of description and context, and I'm not looking to carry your project.
What aspects of the project can you currently manage?
The data? The transport of the data between board? The encryption?
The audio capture? The audio playback?
What type of encryption do you want to use, what are you most familiar with?
Have you decided on a sample rate and block size? How do you want to allow for synchronization of the data?
Perhaps break the project in to steps or pieces which you can manage on your own with the skills you already have?
Retrieving data ...