I installed the vCenter connector and it said "lol, can't upload VM with two disks."
So I disconnected one of the disks and uploaded the VM and now I need to upload the second disk and rejoin it to the VM - if possible.
I thought I might just attach the second disk to a new default VM and upload, but now import says "ClientError: No bootable partition found."
What are my other options?
You should upload the second disk with the API tools that Amazon EC2 provides. Once the tools are set up properly, use
to import your volume to an Amazon S3 bucket. For further help with the API command look here. After uploading it is automatically converted into an EBS Volume. From EBS you can than choose to attach it to an instance.
Another option - which I actually did - was to use ImageX to write an image of the second drive to the first drive, disconnect the second drive, import the VM with the vCenter AWS import tool and then add a volume to the imported VM and use ImageX to expand the image back to the second volume. Worked flawlessly!