For new Vendors I suggest you use the EXPSETUP procedure which is part of the basic NV. It will Import the new Accounts as well as the Notes Information. Of course you must import the accounts before the transactions.
As for the Ap & Sales Journal, I’ve found that when using an external set of books you should Delete the entries after the Import is complete. This way you can make the entries according to dates on the invoices and there will be no chance of duplication when transferring to the live set of books.
Finally I’d suggest the transfer be done Daily. This will keep the Live set of books current and eliminate the chance of loosing transactions if something unforseen happens.