The body can regulate its hormones pretty well in most cases provided the liver and adrenals are functioning properly. This is why I recommend bitters to cleanse the liver. And many of the adaptogenic herbs, that support the adrenals, also help to balance the hormones. In particular suma, wild yam and licorice root.
The minerals boron and zinc, and B vitamins, also play roles in maintaining proper hormone levels.
So these will go hand in hand with the phytoestrogen based foods.
And if you need a boost on your progesterone levels, the herb vitex (chaste tree berry) will increase progesterone after a few months of use.