While viewing the invoices in the inbox you will notice that there are check boxes on the left hand side of the screen, one for each invoice. Just click on these to select a the invoices you need.
Or you can use the master check box at the top of the page to 'select all' invoices on the page or in the inbox.
The 'Actions' button will appear at the top of the page and allow you to process all the selected invoices in the desired way.
When selecting all invoices, AutoEntry will initially only select all the invoices on that page (50 maximum). To select all invoices on multiple pages, click on the warning banner at the top of the page to select all invoices. It will notify you how many invoices in total will be selected.