Ditto on the double sided flannel, it just seems to hold up better. The flannel sold at Hobby Lobby is mostly from A.E. Nathan and is USUALLY pretty good quality, but you do have to watch, especially the prints. (I used to work in the fabric dept. at HL up the street from me and the quality of the SAME fabric would vary from shipment to shipment.) I have not yet ordered flannels online so can't really answer to that, however I think would have confidence in Connecting Threads, but their selection is limited. A lot of others here will have places to recommend.
And yes, ALWAYS prewash and dry flannels (at least once) since the do shrink a great deal and usually significantly more in one direction than the other. That way you will know, as you have already discovered, if any of them are not going to play nice with the others.