1 - Data export functionality provided out of the box by salesforce allows your organization to generate backup files of your data on a weekly or monthly basis depending on your edition. It is mostly used for backup purposes.
2 - Is the upload process something triggered from the Java application itself ? or you need some periodical data dump between your webapp and salesfoce ?
In the first case you have to use the SOAP API interface,directly inside your java code.
find below a good recipe from the cookbook:
http://developer.force.com/cookbook/recipe/calling-salesforce-web-services-using-apex
In the second case you can export your data into a csv file from your java app and load it in salesforce using the Dataloader. This process can be easily batched periodically.