Cal Grant eligibility is based attending a participating California school, income and asset ceilings, and GPA (among the obvious residency requirements, of course). Since the UCs are participating California schools, there is no issue. You would still qualify for Cal Grant.
And yes, the award amount is different between the CSUs and the UCs. You receive more grant aid with the UCs because they have higher systemwide fees than the CSUs have.
Just change the school listed when you know which one you will be attending. You won't lose your Cal Grant qualification (as long as it's a participating California school, of course).