Hi, i was wondering if anyone can help me!

I got a road bike and put Shimano SPD pedals on i,t the same as are on my Mountain Bike, as i only had one pair of shoes that i was using for both MTB and Road. I bought a new pair of shoes (Scott ones) specifically for the road bike and am confused - the sole has three holes in it which i can't fit Shimano SPDs to.....so i am guessing i either need to -
Send the shoes back?
Buy new pedals?
If i need to buy pedals....how do i know which ones will fit the shoes? MTB seems so much more straightforward! Please help