Yes, slow sync will control either the built in flash of an accessory speedlight in the hotshoe.
Why are you using slow sync in bright light? Slow sync lowers the shutter speed to slower than 1/60s, meaning you really risk over exposure of the ambient light and the flash exposure may result in lost highlights.
Just use regular flash sync of TTL-BL and you should be okay. If in doubt, and you just need a little fill, the pop up should be okay. (In that scenario, I use Program mode and the on-board flash with my film camera or D700; on my F100, I use an accessory speedlight - SB28 or SB30)