Thank you for your question.
Actually you can create the category structure and it will be retrieved at the back-end and front-end of your store.
There is no need to create a category structure in the Store Manger and then export it to the .csv file and import back to the PrestaShop through the back-office as the Store Manager should be connected to your database.
In case you have not configured the database connection yet, you should use the Connection Wizard.
Please find more info here:
http://store-manager-for-prestashop-documentation.emagicone.com/quick-start-guide/connection-wizard
Feel free to contact us with additional questions.