It's really better to shave dirt when digging. Take 2-3 inches of dirt over a longer pass. Don't try to hog a bucket full, in the length, or so of the bucket. With the right pitch/angle on the bucket, it will somewhat crumble the dirt, making it easier to empty the bucket. Making a longer pass like that may seem like your not digging much, but a bucket full over that area, is a bucket full, whether hogging with a short pass, or over a long one. And, may save you some time if you pack wetter clay like material, and time spent hammering the bucket to get it empty. That will probably cause more damage than anything.
Doing 2-3 functions at once smoothes operation. Crowd/boom up/curl bucket/swing all at once, can make it so smooth, it will hardly rock the tractor. It's not something you can pick up in an hour, or even a day. It takes hours of seat time, to get progressively faster, and more efficient. Wobble sticks make doing all of those functions at onceso much easier, than on the 4-stick Ford I cut my eye teeth on.
I've never operated a 3pt. hoe, but have operated more than several TLB's, and excavators for over 35 years. On TLB's, it mainly about adjusting engine RPM's, and feathering controls per your skill level. You have to get the feel of the hydraulics, for the amount of work load your doing. For a while, you'll be concentrating on what your hands are doing on the controls, to get said work accomplished. At some point down the road, you'll be concentrating on the boom, stick, and bucket, and it will be more like an extension of your arm, hand and wrist. You won't even really realize the movement of your hands, to orchestrate what you're doing. 99.9% of it is eye to hand coordination. Bottoming out cylindersat the end of it's stroke is probably harder on the machine, than anything you can do. It's going to happen, just learn your machines limitations on reach/stroke.
Excavators engines are pretty much ran at wide open throttle, and have electric, over hydraulic controls. Very easy on the arms, and wrists, just takes a bit to learn to feather the controls when you first get on a different machine, they work so easy. Again, at some point, you should be able to look at the bucket like an extension of your arm, and make the other functions do what you want, from point A, to point B, concentrating on it, instead of what your hands are doing on the controls. It just becomes second nature.