You can remove the "Sync" tag from any contact you do not wish to share with Sync Service. Also, when you import a Now Up-to-Date or Now Contact file, you can choose not to put the Sync tag on the items in the import during the import.

[attachment=0]<!-- ia0 -->import dialog.png<!-- ia0 -->[/attachment]

Simply uncheck the option to "Sync all imported contacts to Address Book" in the import dialog.

Also, keep in mind that Apple provides a mechanism to restrict which contacts are synced to the iPhone through the ability to sync only selected groups to the iPhone. Now X sends contact categories to Address Book as groups, so you can organize your contacts as you wish and only sync certain ones to sync services, then sync only a subset of those to the iPhone.

As for the issue with doing a second import, I would need more information. Does it give an error? Does it stop during the import at some point, or does it appear to complete? Does any information come in, or none at all?

If you like, you can submit a bug report right after attempting the import of the second file using the "Report Bug..." menu option under the Help menu. Along with the information you give in the bug report, it will send up any relevant crash longs, or recent errors.
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Sean Boiarski
Product Manager, Now Software