I seriously doubt that prayer would have any effect on the plants but that is my own bias

. I would propose that the plants-"prayed-upon and non-prayed upon" not be seperated into their respective groups. I would think that this may set up some imbalance due to natural effects, more light for one over another, more moisture, etc. I think if the plants were mixed together with some marking, say a "prayer stick"

placed to mark the plants being prayed upon, this would allow for those natural effects to be mitigated.
by the way, not sure if anyone has mentioned this but why would "prayer" for the plants have to be "in-situ"? Why couldn't someone pray for the plants inside some building away from the plants. I'm sure god is smart enough to figure out which ones are being prayed upon without it being physically pointed out to him like some blind watchmaker.