Shana, hopefully Tanya will come on here and reply as she is more familiar with the downtown malls. I suspect she'll recommend Copley:
http://www.simon.com/mall/default.aspx?ID=784
This mall is quite large. Last time I was there with my teens, we split up, and then had trouble finding each other because I got horribly lost, and then our cell phones weren't working (poor reception). So, if your kids are of an age you are usually comfortable allowing them to go off on their own to shop, I recommend you keep them close and don't separate.
Tanya will explain this better than me, but there are actually two malls that are connected by a pedestrian overpass. One side is your typical mall shops the other is more upscale, high-end shopping (the kind that bores my teens to death - hence why we split up!)
If you're looking for a smaller, easier to navigate mall that is teen and tween friendly, there's Kendall Square mall in Cambridge. It's three stories and a regular layout so hard to get lost in. I like this mall because it has an H&M and a Jacob. If your kids are younger, I recommend (if the weather isn't too chilly) taking the Charles River Ferry that departs from the mall (right outside the food court - can't miss it). It's less than an hour excursion up the Charles and back, but it's fun. Also this mall is near the Museum of Science which is great for kids of any age, and you can get a duck tour cruise from there. I've never been on the duck tour but my kids have (school field trips) and loved it!