Chicken manure is considered hot, which means it's high in nitrogen, and can burn plants. So the common advice is to compost it before putting it on a garden. In practice, with the chickens dropping a little here and a little there, I doubt you're going to have a problem (it's not like there are little burned spots on the lawn where they pooped). But it is something to be aware of.
I wouldn't want the chickens in my garden anytime soon after I planted, though -- whether I planted seeds or starts. They'll scratch up the seeds, pull up the starts, and chew on everything else.
Here's what I do, though. I have the chicken run next to the garden. Both are fenced (I need the fence around the garden for the deer anyway), and the fence in between the run and the garden is more-or-less temporary.
Then, as soon as we finish harvesting in the fall, I take down that fence (just the part separating the run and the garden), and the chickens get to glean everything left behind. It also gives them access to the bug- and worm-rich soil. They have a blast, it cuts down on my feed for awhile, and it helps with the garden. I leave them there until early spring, and then put the fence back up a month or so before planting and till the garden up.