@bdhop Welcome to Mayo Connect, where you can talk directly to people with questions just like yours. A few years ago, I asked this very same question of my friends' daughter, a nutritionist who did research on supplements.
What she explained was enlightening - no matter what you take in, through food or supplement, only a portion is used by your body, and the rest is excreted. Even when you take 500 mg of amoxycillin, for example, not all 500 mg stays in your body to fight infection, a portion is lost. When dosages are calculated, or RDA's are established, the amount accounts for that which the body absorbs as well as that which is lost.
I hope this sets your mind at ease - the doctor was talking about what he wants you to ingest, not what will stay in your body. And just like anything else, more calcium isn't necessarily better. Here is what Cleveland Clinic has to say about too much:
https://health.clevelandclinic.org/too-much-calcium-supplements/
I hope this reassures you that you don't need to walk around all day eating calcium supplements like they were peppermints!
Sue