1. If you build a VMFS on the first HDD cage, but do not format the disks in 2nd cage, then the VSA should only use that VMFS from cage 1 for the appliance. Once VSA is deployed, you can format the second cage as another VMFS and use it as local. * Disclaimer - I have tried this myself, but I believe this is how it should work *
2. My understanding is that ESXi used in the VSA cluster support the same deployment mechanisms as standard ESXi host. It would be good to double check this with technical support however.
3. There is a Replace Node procedure which you would need to run after installing ESXi. Refer to the documentation on how to do this.
I would urge you to spend some time testing items 1 & 3. I'm sure item 1 will work, but haven't tried it. Replace node in item 3 is a tried and tested procedure, but it would be good to familiarize yourself with the steps rather than trying them out for the first time at 3am on a Sunday night! ;-)
HTH
Cormac