Clara never saw Capaldi when she went into the Doctor's time-scar/stream. So I'm thinking Capaldi is the 13th doctor but 14th regeneration (the start of a new set). HOWEVER, Smith's TARDIS still dies and the doctor has to die there, or do something to generate the scar, and it's before Capaldi comes along, hence the lack of him in the timestream.
I think he'll actually die and so will the TARDIS. It's entirely possible the mythos shakeup will add some audiobook/novel concepts such as the Doctor travelling with someone other then Sexy for a while (Compassion, anyone?).
Haven't got a good theory on Capaldi yet, we know timelord have more then 12 regenerations, but number 13 onwards unless assisted/reset end up with severe problems afterwards (This was old-era stuff, remember the timelord that hit number 13 and ended up conjoined with himself?). possibly sexy is dying and assists the doctor in regenerating much like 1->2 (another 50th throwback), potentially at the cost of her life.