This will be my first spring with the chickens, and I only have 6. I am planning on building a fence around the garden boxes (horrid granite-filled sandy Colorado nasty soil over here). I had the chickens out free ranging during the day at the tail end of the season. They left the squashes themselves alone but nibbled on the leaves. They devoured the carrot tops and any greens that had bolted (which was fine with me since they were so bitter). The perennial flowers they left alone. The tomatoes they went crazy for, but I tend to grow indeterminate varieties that grow ridiculously tall, so I train them up a 6ft trellis, so there was plenty for everyone. I took the tomatoes up high, and they took the tomatoes down low. However, toward the end, they used the soil under the plants for bathing, and there were large divots next to the plants. By that time, the plant roots were a good inch around and woody as a shrub, so it didn't bother them, but they would have wreaked havoc on baby plants. I have no doubt they would have dug up and eaten every single transplant I put out.
Now, in the winter, they are going over everything with a fine tooth comb, eating any left over bugs, pooping their poop all over, and it is a good thing. I really don't think you need to worry about there being too much poop. It will have aged all winter, the snow and rain breaking it down. I would take them out of the garden a few weeks before you plant though.