The order of contigs is shown by the order of the lines representing them within the Contig Selector. The order of contigs can be changed by moving these lines using the middle mouse button. Several contigs may be moved at once by selecting several contigs using the above method. After selection, move the contigs with the middle mouse button and position the mouse cursor where you want the selection to be moved to. Upon release of the mouse button the contigs will be shuffled to reflect their new order. The separator line at the point the contig was moved from increases in height.
The contig order is saved automatically whenever a contig is created or removed (eg auto assemble), including operations like disassemble which temporarily create contigs. The order can be saved manually using the Save Contig Order option on the File menu.