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There are organic herbicide options that will kill grass but not flowers, including white vinegar or a dish soap solution. Commercial selective herbicides can also target grass over other plants, but read the instructions carefully to avoid damaging your garden. Herbicides that kill grass but not flowers usually include ingredients like clethodim and sethoxydim. Otherwise, your best bet will be to weed by hand.

Weeds can grow through rubber mulch, but it depends on if you removed all the weeds in your garden beforehand. Weeds already in the soil can grow even when using rubber mulch. However, that doesn’t mean that your garden will be littered with rubber and weeds, but it does mean that the occasional weed might still pop up. Another way you can increase your weed suppression is by using landscape fabric as a second layer. 

Pulling weeds can spread weed seeds and disturb the soil, leading to seed germination. Pulling weeds can also trigger growth in weeds that reproduce through their root systems—disturbing the roots without fully removing them may cause more weeds to grow from the roots.

Very carefully. You should be cautious when using any of the above methods, as any one of them could lead to you accidentally killing desired grasses and plants. However, there are selective herbicides that can target certain plants over others. Look for a product that only affects the type of weeds you want to eliminate and spares the plants you want to keep.