How can i thicken the liquid in my homemade baked beans?

The best way is to simmer the beans on low heat with no lid and allow the steam to evaporate slowly to reduce the liquid to the consistency that you like. Adding any thickening agent will defeat even destroy the taste because the longer you cook the beans, the beans will break down more of its starch and sugar resulting in a more flavorful richer taste subsequently thicken the soup

You can cook it down, on low heat over a long period of time, or you can stir in a solution of cornstarch and water and cook it until it thickens. The first method is FAR preferred. The cornstarch WILL thicken your beans, but it will taste bland.

I don't use the water used to soften the beans or cook them in.