If this is ticked, WICKS will make the card FAT16 bootable, that is the camera will automatically boot CHDK (or SDM) when switched on.
Note that all cameras introduced prior to 2011 require a FAT16 partition to be auto-bootable. Since the largest FAT16 partition is 4GB, larger cards need to be formatted with two partitions.
Cameras introduced since January 2011 can be auto-boot from a FAT32 partition (and thus do not need more than one partition, regardless of size.
Note that only a FAT16 partition can be made bootable with this option. If the current format is not FAT16 and Create Partitions is not checked then WICKS will refuse to make the card FAT16 bootable.