...without soil into a flower bed? the rock bed is extremely deep
doesn't have any natural soil or dirt

I don't need to be cute, but I've seen nice gardens where the rocks aren't hidden, but rather uncovered to become an integral part of the garden. This means changing the design so the plants can go in where there is actually soil or the rocks are deep enough to have at least 12 inches of soil over the top. Sorry, but unless you live where there is plenty of precipitation, you'll need that much to carry over perennial flowers.

Don't think traditional looking yard, be creative. Nature has given you these rocks, use them.

Still, if that's not possible, can you put a simple retention around the rocks and then bring in plenty of soil and compost to make mounds over the rocks. Another yard I know did that creating a series of 36 inch or higher mounds......base about 12 feet from front to back......and planted the mounds in a series of shrubs, roses, perennial flowers. Looked GREAT! Plus having the beds raised, it was easier to tend. What lawn remained was little more than pathways among the mounds/berms.

Short of pulverizing the rock into sand and adding humus, the only suggestion I have is to remove the rock and replace it with soil from some other location. If you don't want to dig the deeper rocks out of the ground, just cover them with ~ 6 to 8 inches of soil. Should be adequate for flowers.

How big are the stones, why is it so deep? Do you want rocks to go away? Make pockets of soil and add plants which are native to your soil, where ever you are. Do your homework on plants before you go through the labor. Is there another location in which you can add flowers. Is there water available to irrigate if needed?