The problem with work is the word we use for it. Since we work everyday, we're used to associate "physical work" and "effort", and that's confusing.
Physical work is a well defined quantity, but it needs 3 surnames, and this is usually omitted. You must specify these three parameters:
Work done [by some force] [on some system] [along this path]
Note how deep is this sentence. Work is done by forces, not by people. You don't do work, a force does work, not you.
Plus, work must be considered on a system. If you lift a rock, you are doing possitive work on the rock. However, gravity is doing negative work on the rock.
$W_{you}=mg\cdot h\cdot 1$; because $cos(0º)=1$
$W_{gravity}=mg\cdot h\cdot -1$; because $cos(180º)=-1$
So the total work on the rock is $0$ and that's why you are not increasing its kinetic energy. If you perform extra forces, then you will accelerate teh rock ($F=ma$, you know). So you'll accelerate the rock and hence the KE changes. It makes sense.
But you have to realize that you are considering the rock as a well delimited system. If you include the chemical energy stored in your arms, then your system under consideration is not the rock alone anymore. Your new system under study will be the rock-person system, and then you have to consider ALL forces involved in that system, not just your arm.
In conclusion: work needs 3 specifications. You seem to be needing to focus on the "on what system" part.
Hope this helped