I have done a quilt and flame veneer guitar. I agree with Ricky mostly.
I do a light sand with 400 grit then rub with metho looking very carefully for glue spots, A light sand on some glue spots may be necessary. GooOff will be needed.
The metho will raise the grain very slightly so need another 400 sand. Then as Ricky said thick dose of stain and wipe off most with metho. It will leave the quillt nice and dark. Can do it a couple of time if necessary. Then the recommended mix of stain. I do not use water.
You can see some of the issues I had with my guitars in the Build Dairy's in the signature block below.
I am still very much a learner but you will learn fast. Well worth the effort and take your time, search this forum incessantly. There are many very experienced members who have done it all before.