Does the ESXi box boot another OS to gain access to the programs you're storing on the 2nd drive? Is there anything on the 2nd drive that you want to keep, or do you just want to blow everything away and make it available to create a VMFS partition?
If you just want to blow alway everything on the 2nd disk then you have a couple of options:
If the server has a disk controller that is capable of initializing drives (i.e. a RAID controller) then just use the disk controller interface to re-initialize the drive. Then when you start up ESXi, connect with the VC client and go into Configuration, Storage, Add Storage and configure up a new VMFS partition using the entire disk
If the server doesn't have a disk controller capable of initializing drives and the server doesn't have another OS installed that can re-partition the disk you can use the "unsupported" ESXi console:
At the ESXi "gray and yellow" console screen, hit <Alt><F1> to get to the console screen
Type "unsupported" (without the quotes) and hit <Enter>. You'll be typing blind so don't expect to see what you're typing. Once you hit <Enter> the shell prompt (#) will appear
Type "fdisk -l" to get a list of the disks and partitions
Type "fdisk diskpath" where diskpath is the path you identified in step #3 (i.e. /dev/disks/vmhba1:0:0:0 (the last 0 indicates that you want to work with the disk as opposed to a partition on the disk). That will get you to the fdisk prompt
From the fdisk prompt you can use "p" to see the partitions on the disk, and use the "d" command to delete the partitions
Once you've deleted all the partitions you can get out of fdisk and type "exit" to close the console session (you'll just get a blank line with no "#" prompt
Hit <Alt><F2> to get back to the ESXi splash screen
Go back to the VI Client and go into Configuration, Storage Adapters, highlight the storage adapter and do a Rescan. Verify that the disk shows up
Go to Storage, Add Storage and configure up a new VMFS partition using the entire disk
