It generally is the best path to results, actually. You don't need to be friends with your pokemon, but having a degree mutual understanding and trust can make a considerable difference, the same as working alongside a fellow soldier, for example.

*and yes, he's speaking from experience on that point...*

But for specifics, that's up to you to determine what works best. If you have a pokemon that likes a particular kind of treat, for example, simply making it clear that it won't get any if it causes trouble may be plenty to get the point across. Removing privileges in general tends to be an effective motivator for many, really. Or in some cases, even simply showing disapproval or disappointment--or the appearance of it, even if you don't particularly care--can suffice.