I made my one and only bag from denim which is sturdy and strong and excellent for maintaining snaps. I bound it with a print to add some excitement because I also had some applique on the front. You can attach the magnetic snaps before putting the two layers of the bag together (lining and outer). Just work out where you would like them and mark the spot on both the female and male sides (the snaps have two parts you need two spots that meet up together to maintain these parts). I use the magnetic snaps that are a little like a split pin at the back. They should have instructions as to how to attach them but I just make a small slit at the spots I want the parts to go, insert the parts and split the pin at the back which will hold the part in place.
The trick is to not place them too close to a seam!! Your machine will not like you for it!
But I do assure you that when you have them in and the outer and lining are together with the bag all made up you will only see them if you open the bag up to get something out of it.
When you attach the parts one side of the snap will be on the outer part of the bag where the pockets are and the other part of the snap will need to be placed on the lining part of the flap.
I hope this helps and I hope you feel well again soon.
Tamara