Can I import data into a custom entity that has a N:N relationship with the Account entity?

Hi, We are in the process of doing our original migration of contacts and accounts to CRM Dynamics 2015. I have created several custom entities to hold "taxonomy" information on the accounts. These custom entities are in a many to many relationship with the accounts entity. I would like to import the values for the custom entities, but am having two challenges:

1. The custom entities do not show up when trying to map fields.

2. I don't know the GUID of the account that has been created when I imported the accounts (I know the ID the previous system gave the accounts).

Is what I am trying to accomplish doable?
Why are my custom entities not available for import?

Thanks,

Veronica