The two options you specify control the automatic execution of Code Analysis on managed and native C++ respectively.
Code Analysis of managed code is performed by FXCop engine analyzing the generated IL.
Code Analysis of native code is performed during compilation by the PreFast engine analyzing the C++ source code.
I STRONGLY encourage you to require your developers to have run CA on their code BEFORE checking it in. If you don't, you're:
1) Delaying the process of ensuring that your code has no known vulnerabilities and issues that could otherwise have been systematically removed from your product's source.
2) Denying your developers their right to improve their skills by learning incrementally what code they should NOT be writing and why.
3) Selling your customers short because they're the ones who will suffer from crashes and security issues when they're using your product.
Further, if you're writing native C++ and have not already planned to start adorning your code with SAL Annotations, then, frankly, someone at your place of work deserves to be dragged out into the street and humiliated! There's some GREAT stuff coming down the pipe shortly in the next version of the SAL annotations - get on it now and be WAY ahead of the curve vs. your competitors! :)