Hi James,
Pls see below:
1. Yes, you can directly type in the API name for the field if you don't see in the dropdown. For the "External Id" field specifically, pls note that the Integration App already has logic built-in into the code to set a defined format for each appropriate NetSuite record type to prevent de-duplication of records and you not need to map this explicitly in mappings.
2. Once a quote is marked primary, the quote lines should mirror the opportunity lines. You should be able to map the Opportunity lines directly. Does this address your use case or is there something else you were looking to achieve?
3. Here's an example on how to do this: https://connective.celigo.com/t/stop-individual-salesforce-accounts-from-syncing-with-netsuite-customer/1434. We will also be adding a separate article in our Knowledge base.