Hi Suzette, if the batting is thin enough along with the cotton I'd put them in the hoop. If you find the hoop doesn't sit well ie. it's a bit hard to put the fabric in it then I'd try the basting stitch and just lay the fabric on top. Have a go at both ways and see what is best for your hoop and machine. You'll soon find out what is best.

If you need to have a look at one being done - type in Google "quilt in the hoop tutorials". Love and blessings Chris

I have a special 150x150 mm hoop for my Designer that has two inner rings, the smaller one ideally fitted to hoop both batting and fabric.
Using a 'normal' hoop try if it will accommodate the two together - I often find it hard to hoop a thick towel and would not hoop batting + fabric together.

Are you putting you backing in there too? I would do all three together and if your hoop isn't the do all quilters hoop, or something similar, then I would certainly baste it to the hoop. Trying to make it fit in one of the other hoops could be impossible to do. Don't forget to share your project!