Ahhh the black art of flash - Vodoo with a capital V.
My 2 cents worth & will stand corrected.
With regard to your specific question the on board flash should still work in the same manner as the SB910 in that irrespective of your settings be it Manual, P, A or S it will perform as you dictate it to do via the Flash option in your custom settings menu / Flash Control for built in flash - Least thats how it's done on those I have used - D70s, D200, D300s, & D7000 so I'm assuming it's pretty much the same on your 800. Within that option you can specify the on board to be TTL, Manual (you then have a further option to specify the level of output manually, repeating flash (i'm assuming this is for strobe style stuff - check your manual) or as a commander flash for wireless work with other compatible flashes.
For a more general overview of the black art have a look at http://strobist.blogspot.com.au/
- particularly the Lighting 101 - it's a series of tutorials on strobe work - by no means the be all and end all but not a bad place to start if you want to go down that path.
I have just started to dabble and some of the things to consider are at odds with available light work which just adds to the mystery but I reckon it will be something with unlimited potential if I persevere and free up my limited imagination.