Question
I recently laid out scott's weed and feed on my lawn and i accidently spread some over some newly planted morning glory flowers and they died.  My question is was that the reason they have died?  If that's the case,  do i have to totally clean the soil where the flowers were planted and start anew?

Answer
My experience tells me that the weedkiller in the W&F has killed the morning glory (I trust that you have identified the plant accurately).
Depending upon your turf, the W&F product would have "2.4D" or "Atrazine" as the weedkiller.
2.4D is easier to get rid of; cultivating and aerating the site will most likely render it safe in about three weeks.
Atrazine is a different matter. It is persistent and is liable to find its way into groundwater eventually. I suggest laying down a fabric which will allow water to pass through and putting down a layer of clean soil to grow the new annuals. The objective is to slow down root penetration into the old soil. In the meantime the atrazine will be broken down to a level which is safe for your plants. I'd say 3 months.
And if this seems like over cautiousness, all I can say is "There is no cafe chemical; only safe ways of using chemicals".