Whenever you import a new style, it exists in parallel to any others you have; that is, it and your other styles don't have any effect on one another.
As such, yes, you'll lose any changes you made to your first template -- they'll have to be reapplied manually to the new style.
Administrators by default have a Quick Style Chooser dropdown in the lower left-hand corner of the forum through which you can choose to view the forum using any installed styles.
You can easily change your default style through the vBulletin Options -> Styles & Language Settings menu.
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