To avoid any ambiguity or hint of sexism, most modern speakers keep the two senses of בעל strictly distinct as follows:
When בעל has the sense of husband, it is always inflected to indicate a possessor. In the case that its possessor is not a personal pronoun, this produces some redundancy; for example, "Miriam's husband" is translated as בעלה של מרים(ba`aláh shel Miryam), which literally means "her-husband of Miriam". (This sort of construction can occur with other nouns as well, but usually only in more formal contexts.)
When בעל has the sense of owner, it is never so inflected.
However, some speakers do consider it sexist to use בעל with the sense of husband after all, instead preferring the word איש('ish, “man”), as it is more directly analogous to the word אישה('isháh, “woman, wife”).