Some Amish ladies hand-quilted one for me several years ago with a layer of flannelette as the batting.
You asked about quilting tips, the ladies said it was quite easy for them to hand-quilt.
If you are machine quilting, there would be no difference in how-to's.
Just the normal, test first re what threads, tensions, etc. would be best.
Mine only has one layer, but I see no reason why you could not have two of flannelette.
Likewise, no reason why you could not have flannelette as both your backing and batting.
Mine was regular quilting cottons for the pieced top and backing.
I have liked it for the drape and "feel" of it when I use it.
It certainly has not created any problems over the years.
For sure, I would recommend a hot water wash and hot dry, to deal with the shrink factor.
Like any fabrics, bleeding could be a problem with flannelettes.
As you guessed, deal with that as you normally would.
One thing to keep in mind ... if you are wanting loft, you will not get it with flannelette.
Although, I guess you could, if you used more layers than the single that I have.