I am still learning with invisible thread but I do use it quite often and for some effects I really like it. I keep reading that thread weight plays a big role in the success of your stitching...maybe the polyester in the bottom is just too heavy to stitch with the monofilament? I would definitely try using it in the top and bottom both and see how that works...at least to get through this current project of yours. After getting comfortable with that maybe experiment with other finer threads in the bobbin on scraps to see if you can find a pair that work well together.
I would like to try the sulky monofilament, but so far have only used the inexpensive Dritz brand sold in Jo Anns quilting section. ;) Good luck!