The smaller PCI-E work in the larger ones, just make sure it fits..small factor or large facor on the machine. In the bios you should be able to tell what device you can boot from and the card has its own bios.
I would actually recommend using the QNAP with NFS if you can, this way you can add additional ESX hosts to the same NFS share or iSCSI LUN and get the VMs running incase the host itself dies.