Just lay the sill plate next to the anchor bolts, make a straight line using you speed square. Just place the speed squarely on the 2by and **** it against the anchor bolt.
Then place a short scrap 2by whatever on sill lined up with the outside line of your building (where the sill plate will go) and then measure this distance. Mark this distance on the previous line that you drew on sill plate.
Now drill your hole (half the anchor bolt diameter) over from this mark. Note: if you are using 1/2 anchor bolts, drill a 5/8" hole. You need some wiggle room to get the sill plate perfectly placed.
The place and bang method mentioned above will probably work, but you will need two people to do the job. I would use a level or block to make sure you are actually holding the sill plate above where it really needs to go, since you have a few inches of air space.
Good luck, I just place 122 ft of sill plate on my stem wall last week. I got the first floor walls framed, this weekend, we start placing the wooden I beams for the second story.