I brought home my maltese pup at the age of 16wks, well she hates our saint bernard and growls and barks constantly at him.   Saint is no aggressive with her at all but as soon as he goes near the maltese she freaks out

Unfortunately she obviously ahs not been socialised with big dogs by the time you had her, and it will take longer now for her to adjust to him, but in time she shoudl be OK.  You need to praise ehr hwnenever your big boy is around and only have her as close to him as it takes for her not to freak.  Gradually she shoudl get used to him being around especially if he will ignore her (distrat him with training, a game or treats).  Having her in a crate may make her feel safer as slong as she doesn't guard it.