I'm not sure I can answer that. I think yes, they were basically completely separate schools before Xavier was built, but since my kids were younger I don't have direct experience. From what I remember hearing in the community, though, they were stand-alone high schools with no connection ... there was a significant eastside/westside rivalry back in the day, and the image of the schools kind of played into that (LaSalle was considered more working-class and Regis had more of an upscale image, from what I've been told, which also fit into the stereotypes of the east and west sides of Cedar Rapids in general).
As you might imagine, there was quite a bit of drama over the creation of Xavier as a single high school, with a lot of families fearful that the histories and individual images of Regis and LaSalle were going to be swallowed up and erased by Xavier ... a lot of graduation parties the first couple of senior classes of Xavier still prominently featured the colors of Regis or LaSalle, depending on where that student had come from.