I personally have found that the quilt store fabrics are a higher quality, but I have bought plenty of Joann's fabrics because they are such good prices and they do have a really nice selection. Also, since they purchase their fabrics in such high quantities, they are able to sell them for a lower price.
I would suggest that you don't intermingle the fabrics - if you start a project with joann's fabrics, complete the project with it, and if you start with the quilt store fabrics, complete with the quilt store fabrics.
If you do "mix" the fabrics, I would recommend that you wash and dry the fabrics first to pre-shrink the fabrics in case there is a real quality difference between the fabrics!
I have always found that it is just easier to buy what you like - because then you will use it!!