I assume that by "white list", you mean temporarily bypassing Gatekeeper (which prevents apps without an Apple certificate from launching). It's really easy to do on a case-by-case basis. Read
How to bypass Gatekeeper in OS X Mavericks. Even though it says Mavericks, the same procedure applies to Yosemite and El Capitan.
I can't offer a suggestion about making a schedule to index Spotlight. AFIK, it updates itself automatically, on the fly.