I quilt and there's a difference between a "quilt" and a "comforter", so that might be why your directions are confusing. A quilt is generally 100% cotton for the top and backing but can have batting that is cotton, polyester, or some kind of blend. Quilts are generally pretty flat, not poofy. A comtorter is poofy and has lots of "loft", which you can't get from a 100% cotton batting. Comforters are probably (?) always filled with 100% polyester, which you can't really iron with a hot iron 'cause it will melt. Polyester doesn't breathe well, I would not use it for a baby quilt 'cause it also doesn't wash as well either and is much harder to sew through.
So, here's what I'd do. Go to a local fabric store / quilt shop and buy 100% cotton for the top and bottom layers of the quilt in whatever cute print you like. (Flannel can be extra comfy and works fine!) Buy either 100% cotton batting or a blend that is mostly cotton, so that you can iron it. The batting should come with instructions about how densely/closely you need to quilt/sew it. Generally you need stitching every 2" to 4" across the whole quilt so that it doesn't come apart with lots of washing.
Um...lets see, this post maybe needs to be longer than I have time for right now, 'cause I'm thinking about explaining how to baste the layers together and do the sewing, etc. You can actually get simple books for beginners that have patterns for baby quilts and explain all the little steps involved from start to finish, so I'd recomend you get an easy book. I guarantee Joanne's will have one. A book will also give size suggestions. You don't need to "piece" a quilt from lots of little squares, you can just use one fabric for the top, but you'll still need to stitch or tie it, and a book will explain that. The Quilt in a Day series is good to read too.
See if this is enough to get you started and feel free to pm me with questions as you go. Look out though, quilting can be totally addictive and an expensive hobby if you do a lot of it!
Good luck! I absolutely believe babies and children should have hand made quilts and toys around them. Enjoy the process of making something special and don't try to make the first one perfect!
(shamless plug for my website)