There is a bracket with 2 10mm bolts that have special washers to keep out water.
Don't drive very far without the covers on. I made this mistake when I bought my roof rack from another forum member. I took the covers/brackets off the night before the 4.5 hour drive and it whistled non-stop. I had a very bad headache by the time I got there.
The bolts to fill the holes without a roof rack are shorter than the bolts that hold on the roof rack.You also need rubber backed sealing washers,I think they come in a kit from Toyota.The white plastic pieces are for asthetic purposes,to make it all look better.I used sealing washers from Ace hardware when I installed my used roof rack with some black RTV to be safe.Hope this helps.