if your plan is to eat a proper meal at Eataly, i'd suggest getting your name on the list as soon as you arrive. there'll likely be a wait for a table, so spend the time shopping around. the pizza/pasta counter is good, but could be redundant if you're going to Motorino later. the vegetable counter is probably the most interesting, food-wise, of the ones i've tried.
personally, i'd go for the standing tables in the piazza. it's the most lively and feels least like dining in a mall food court. it's bustling and loud and good for people watching over a glass of wine.
the rooftop is disappointing in that it offers almost no view, even during the summer when the roof is more retracted. it'd be worth visiting if you're really into beers.
don't gloss over the produce section. it's by far the best part of Eataly, even if you're just looking. they have some fruits and vegetables that are otherwise impossible to find.
We love Motorino and usually get the Margherita pizza. The side dish of meatballs gets a lot of recs but I did not think it was special.
They can get very busy so get there early. The place is small.
You might want to try Keste in the W Village. Also excellent pizza and a little bigger so the line moves fast. Keste also has a more varied non pizza menu. I love their truffle barata!!
I usually get to either place around noon time when there is no line.
As for Eataly, I find it overwhelming.