Where is the thread bunching - are you getting nests under your fabric? If this is the problem, your issue is NOT with your bobbin thread, it is with your top thread. Take ALL the thread completely off your machine and re-thread. Make sure there are no little threads stuck in your tension disks. Make sure your thread isn't getting caught on something. Sometimes my upper thread gets hung up on the handle.
Wouldn't hurt to re-thread your bobbin also, check under the spring in your bobbin to make sure there's no thread stuck there, either.
What size needle are you using? You might consider going up a size, especially if you're doing FMQ.
Regarding the thread - "stacked" means it comes off the spool evenly, from top to bottom. "Cross threaded" means it crosses up and down the spool as it's wound. If you're using C&C, it's stacked.