Most basic answer: Don't enable steam cloud, ever.
Let's say you had steam cloud enabled yesterday, decided to hack today (thus having the cloud turned off), hacked a bunch of levels/prestiges, then turned the cloud back on the next day. It'd be a little suspicious seeing your account get 5 characters to prestige 3 in the span of 2 days, right? When you enable steam cloud, you let steam see your files/data. It's been rumored that people have been banned from devs that look at steam cloud data and through logic/reasoning see if you hack or not.