You should probably be using UR anywhere between 7 and 10 stacks of screech (some people will recommend waiting for a trinket proc to let off banked embers but I've found you might just be waiting in vain most of the time), and with it glyphed it should be back for when the bats are back. Though timings are completely dependent on how your healing rotation works and how many stacks you push it to.
As long as you aren't getting interrupted very much and you aren't ever capping embers then you're doing most things right. If your dps is low it's probably as much a reflection of the annoying mechanics of the fight for a caster / your own bad luck with procs. And don't consider aoe damage on bats boosting your dps being a bad thing / "padding" - getting them down quickly is VERY important and if you are the most effective player in that regard then you are more than making up for your place in the raid.