It really doesn't matter (technically), but it probably will be easier to start with yourself and enter your parents and your siblings and then enter your paternal grandparents and your maternal grandparents and their families and work backward by generations. There is no reason to separate your paternal and maternal lines by creating separate trees -- the software will enable you to do this when you want to share information on one particular line but not the other or to look at (or print out) your trees and family groups in various ways. These options are in the "reports."
If you have children, then you might want to start with them and enter your line and your husband's. Again, the software will do the "sorting" and "reports" for you. That's the great thing about genealogy software.