If I have decided to switch from pre-med to business but am taking science courses this year, should I apply for pass faily option on my sciences to protect my gpa, or will that look negative on my part?
Talk with an advisor in your School of Business. It may be fine, but business does have some math and science requirements (which you may or may not yet have satisfied). As long as you met your college requirements, no one will care if you took a (extra) science class as pass/fail.
Do you have to apply to a particularly competitive business school within your college? If not, then I wouldn’t worry about it. GPA is much less relevant to business than to pre-med.