Once chinchillas get used to their environment, there will be few instances where you actually must pick them up. Our chinchillas are very good about going into their cage with little prompting. If you can maintain a consistent schedule, you'll find that the chinchillas will go where you want them to without any prompting at all. For us, this means that around our bedtime the chinchillas will run in to their cage and await their nightly treat (e.g. a raisin).
However, it's hard to resist the temptation of picking up your chins. If for no other reason than to feel their incredibly soft fur. So if you're going to pick up your chinchilla, you might as well do it the right way. That is, scoop them up from below and always support their back legs. We also like to keep them close to our bodies so that they're less likely to jump.
What you want to make sure you don't do is pick them up by the tail, squeeze their bodies too much, grab them by their ears, grab them by the neck (like a cat), or bring your hands down on them from above. All of these actions will agitate your chinchilla and can lead to harm. We've also noticed that they have good memories of stressful situations and it requires a day or two for them to trust you once again.
Our chinchillas also like to have their heads rubbed in between their ears. They also sometimes tolerate gentle chin and belly rubs.