If I now have guardianship over my mother with Alzheimer's, does that trump my stepfather's Power of Attorney over her?

If you were appointed as Guardian of the Estate of your mother then you are responsible for collecting and inventorying your mother's assets as of the date of your appointment. You should contact each financial institution that holds one of your mother's accounts, or held an account at the time of your appointment, and advise them of the creation of the guardianship, your appointment and to change the title to the account to reflect the guardianship and your authority. If your stepfather has transferred assets of your mother after your appointment as guardian of the estate you should consult with an attorney regarding action that can be taken to collect the assets for her guardianship estate.

If you are court-appointed guardian, you should have your own counsel to ask this question. This issue most likely should have come up and been addressed when you were appointed. Discuss with your attorney immediately.