I've been doing this with our five chickens for several weeks now, and yes, they do get used to the routine of moving from their coop/run to their tractor in the morning, then back to their coop/run at night.
From time to time I'll have a problem with one chicken or the other (usually it's Billina, our d'Uccle, who'll decide to make a break for it), but I've been really surprised at how easily they've figured out what they're supposed to do.
The problem comes when I break the routine. My tractor isn't roofed, so several times I've run out midday to transfer them into their roofed coop/run. This isn't their routine, so they aren't quite sure what they're supposed to do, and I have ended up chasing them all over the yard.
Then, again, if I can get at least two chickens into the coop, the rest will usually follow. Fortunately, two of my birds are hand trained (they'll step up onto your arm), so I can easily nab these two.