If I am understanding you correctly, you want to put backing and batting on the machine and then each pillow "case" will be a separate thing??
in that case it should be 'doable'... you can either 'float' each top one at a time... IOW, do the first one, wind it, float the second one - do it, keep winding, etc etc... just make sure you get each top 'floated' good and straight - probably by pinning (just don't run over the pins)
another way would be to scant stitch the tops together and treat it as one big top then cut them apart - you could do this by having an extra say inch for each of the sides you stitch together or even cut strips to do that
we did that when first doing our practice quilting - stitched two fabrics together - treated it as 'one' then cut the finished stuff up into lap quilts