Ask Mr. Smarty Plants

You have discovered for yourself that magnolias are allelopathic to other plants.  This means that the magnolia produces chemicals that inhibit the germination of seeds and growth of plants that are potential competitors for its resources.  The roots and fallen debris (leaves, flowers, etc.) from the magnolia tree contain substances that limit the growth of other competing species that grow underneath it. In the case of magnolias, the substances are sesquiterpene lactones—costunolide and parthenolide—(see Abdelgalel, A. M. and F. Hasinaga.  2007. "Allelopathic potential of two sesquiterpene lactones from Magnolia grandiflora L." Biochemical Systematics and Ecology Vol. 35, no. 11, pp. 737-742.)  A complicating factor is that many plants won't grow in the dense shade created by the magnolia tree—or any other tree, for that matter.

Walnuts trees (Juglans sp.) also have allelopathic effects on plants growing beneath them.  The substance produced by walnuts is called juglone.  Virginia Cooperative Extension has an article "Trees for Problem Landscape Sites -- The Walnut Tree: Allelopathic Effects and Tolerant Plants" that offers some tips on reducing the effects of juglone on plants growing near walnut trees that could apply to your magnolia.  One important tip is to "Regularly clean up all fallen leaves and fruit..., keeping debris away from desired landscape plants."  They also list plants that are tolerant to juglone.  These, of course, are NOT guaranteed to be tolerant to the sesquiterpene lactones in magnolias, nor are they necessarily native to Southern California (nor, for that matter, are any of the Magnolia species). 

I could find no list of plants that are resistant to the allelopathic effects of magnolias.  So, my recommendations to you are:  1) keep the debris from the magnolia cleaned up from the area where you want the flowers/plants to grow, and 2) choose native plants that are shade-tolerant.   Here are a few recommended shade-tolerant herbaceous plants that are native to San Diego County or an adjacent California county:

Apocynum androsaemifolium (spreading dogbane)

Argentina anserina (silverweed cinquefoil)

Athyrium filix-femina (common ladyfern)

Claytonia perfoliata (miner's lettuce)

Fragaria vesca (woodland strawberry)

Lobelia cardinalis (cardinalflower)

Maianthemum stellatum (starry false lily of the valley)

Polystichum munitum (western swordfern)

Pteridium aquilinum (western brackenfern)

Viola adunca (hookedspur violet)

Apocynum androsaemifolium

Argentina anserina

Athyrium filix-femina

Claytonia perfoliata

Fragaria vesca

Lobelia cardinalis

Maianthemum stellatum

Polystichum munitum

Pteridium aquilinum

Viola adunca