Correct me if I'm wrong but I don't think any of the parts in the current Mac Pro are internally upgradable. OWC might have an upgrade option for the SSD though.

Otherwise you've got to put everything through the external thunderbolt 2 ports. They're fine for storage and there's been some progress on using them for home made gpu expansion boxes but really you'd be better off waiting for Apple to offer something with thunderbolt 3 or internal pci card slots.