On second thought, it was the practice at the time to have seperate people serve as Guardian (physical custody of the underage monarch, with responsibility for education and upbringing) and Protector (wielding royal authority and managing the affairs of state on behalf of the underage monarch). For example, during the brief reign of Edward V, his mother the dowager Queen served as Guardian while his uncle (the younger brother of the late King) served as Lord Protector.
This practice broke down following the OTL death of Henry VIII. Henry's will named Edward Seymour, Earl of Hertford (the young King's uncle on his mother's side) as Guardian and appointed a regency council of 16 members to jointly exercise the duties of Protector. Shortly after Henry's death, though, the regency council voted 13 to 3 to dissolve itself and appoint Seymour as the sole Lord Protector.
Assuming the prior practice doesn't break down ITTL, Catherine would likely be Guardian of Queen Mary, while Wolsey or Suffolk served as Protector. Alternately, if Catherine took power as Lady Protector, there would be a significant push for her to surrender custody of Queen Mary to a different Guardian.
Of course, the practice might break down ITTL as per IOTL, but if it doesn't, I'm not sure whether marriage arrangements would be in the hands of the Protector, or of the Guardian, or if they'd require the consent of both responsible parties.