A family of Microsoft relational database management systems designed for ease of use.
It sounds like you created the table before importing. If you start from scratch with nothing in the new database, then import the tables you want into the new database, the Autonumber will come across too.
I thought your tables were already split from the database with the forms, reports, etc. If I was wrong, then you should definitely do as ScottGem said. If you have the tables and relationships in their own database file, it's likely that your original question becomes moot. The huge point here is that you really can only survive with one set of tables. It's conceivable that your data can stay on life support for some time with two sets of tables, but it will be difficult and way over your head until you learn how to deal with all the complexities implied by your original question.
If your messy kitchen database is not split, I think your best approach would be to split that database before even thinking about other changes. Once it is split then the old front end can stay in use while you create a new cleaner front end