it is your choice- but if the flannel is single sided- or thin i would add batting- it just makes the quilt softer/fluffier cozier.
flannel is nice to work with but the thin stuff can be a bit stretchy- add starch- and press carefully- do not iron around on it-and stretch it out of shape-
some of us use flannel in lots of our quilts- it makes them soft and wonderful.
for baby quilts i usually go for a good (lofty) batt instead of the heirloom thin batts...they hold up better- and with baby quilts you want them to hold up.... warm & natural is a good choice- or dream poly is wonderful