I think you are waiting alittle too long to start the wind down. Usually when they rub eyes/ yawn, they are VERY tired. You might try to get into the wind down about 10 min before you think they will be tired.
What has worked for my dd is really relaxing music. I have room darkening drapes over the windows and a sleep sac she sleeps in. We go in and close the drapes, put on the sleeping bag and sit in the rocker with the music going. Sometimes it only takes one song but other days it could take 5!! I wait until she stops wiggling and seems to relax and then transfer her to the crib. Most of the time she will roll over and drift off, but there are times that are not that smooth. Just go with your instinct when that happens and do your best. My belief is that if they are able to drift off most of the time, those few times you pick them back up and settle some more will not hurt. JMHO!
ALso, read the sticky at the top of this board. It will give you more ideas about naptime!
HTH.