If you have already filed for a divorce, legal separation, or paternity the petition for a protective order should be filed with the judge presiding over that issue.  The process for filing the petition and any hearing is the same.  In an emergency situation, even though you have a divorce pending in one court, you can still apply for a protective order from another judge.  The law requires that judge, after entering an ex parte protective order, to transfer the case to the judge presiding over your divorce.