Yes they should be somewhere in the box.
Does the Toto Drake toilet come with those plastic bolt covers to cover up the flange bolts or do I have to buy those?
They're plastic covers. Note that the plastic bit that fits under the nut must be the right side up for the thing to snap in place. Try it first before installation to may sure you get the right orientation, or it won't snap on. The lip must project up; if it is flush with the base of the toilet, the cap can't get under it to snap in place.
Important note - I'm not a pro
Retired Defense Industry Engineer; Schluter 2.5-day Workshop Completed 2013, 2014
usually inside the tank in a plastic bag.
Thanks guys! I found them in the plastic bag that comes with the tank. I'll be sure to get them on the right way.