Answer: Your first step would be to remove the weeds. You can pull them or use an herbicide containing glyphosate. Read and carefully follow the label directions, including the recommended waiting time between spraying and removing the weeds. This is important because the chemical has to move from the foliage down through the plant to the root where it kills. Another option would be to cut them off short, then smother them with damp newspaper topped with organic mulch.
If the existing rocks are large, you will need to remove them -- rake and shovel are usually required. If they are a fine gravel, you could dig them into the soil.
You will also want to work in ample amounts of organic matter such as compost, rotted leaves, well aged stable manure/bedding, or milled spagnum peat moss to amend the soil prior to planting. It is also a good idea to run some basic soil tests to check fertility and pH. Your local county extension should be able to help you with the tests and interpreting the results.
If you are growing bulbs and perennials, it is not practical to use weed netting as the plants become entangled in it and the bulbs are not able to come up through it. Instead, a layer of organic mulch several inches thick is more beneficial to the soil and to the plants. It will break down slowly over time and add organic matter to the soil while it helps keep down weeds. It also helps keep the soil more evenly moist during dry spells.
It is certainly not too late to plant! September/early October is a good time to plant many perennials, and spring flowering bulbs should be planted in October once the soil temperature has cooled a bit. Enjoy your new garden!
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