are you talking about cotton/poly batting???
or a cotton blend fabric?
you can use any fabric you want to= you need to pay attention to care instructions- beyond that you can put it together...in other words- if one fabric is dry clean only and one is throw it in the washer and dryer- you probably don't want to put them together- if however everything can be cared for the same it works.
i mix cottons and wools alot-and silks-