It all depends on what you wish for your quilts in the future. Nylon thread will eat cotton. It is not open for debate. Now, do you care? Do you want your quilts to last for five years, ten years, a hundred years? Your call.
1.) Use like thread top and bottom matched to the fabric you use.
2.) Use like thread top and bottom, regardless to the fabric you use.
3.) Use whatever is cheapest.
One gives you most permanence over the long term. Three gives you the least. Second gives you a huge variance depending on use and cleaning of the quilt.
tim in san jose