@igorcraven with quarry levels alone it gives +1 per level for output. +1 is literal so if you get 10 stone you'd get 11 at level 1, 12 at level 2 and 13 at level 3. These upgrades are really focused on the more rare metals. A quarry that gives 1 hqm per cycle would give 3 at level 3 which is huge.
The output is also increased based on your mining level. At level 100 output is almost doubled.