What I've been telling the students in the intro mechanics class I TA is that each force corresponds to some amount of work. The individual contributions of work add up to the net (or total) work, just as the individual forces add up to the net force.
So, for instance, when you lift a box up from the floor to a table, there are two forces acting on that box: the force $\vec{F}_\text{lift}$ you apply to lift it, and the force of gravity, $\vec{F}_g = -mg\hat{y}$. You can calculate the amount of work done by the lifting force as
$$W_\text{lift} = \int_0^h \vec{F}_\text{lift}\cdot\mathrm{d}\vec{x}$$
and you can calculate the amount of work done by the gravitational force as
$$W_g = \int_0^h \vec{F}_g\cdot\mathrm{d}\vec{x}$$
In a typical physics-problem scenario, you would be lifting the box at constant velocity (except for the brief moments when you start and stop its motion, which I will ignore for now). In this case, you could draw a free-body diagram and use Newton's second law $\vec{F} = m\vec{a}$ to discover that your lifting force has to be equal in magnitude and opposite in direction to the gravitational force:
$$\vec{F}_\text{lift} = mg\hat{y}$$
Armed with this result, you can calculate the work done by each individual force (try it!): $W_\text{lift} = mgh$ and $W_g = -mgh$. The net work done is zero.
You can just as well calculate the net work from the net force,
$$W_\text{net} = \int_0^h \vec{F}_\text{net}\cdot\mathrm{d}\vec{x}$$
In this case, the net force is $\vec{F}_\text{lift} + \vec{F}_g$, which is zero (because the box is moving at constant velocity, remember $\vec{F}_\text{net} = m\vec{a}$). So, again, the net work is zero.
"But wait," you say, "I thought the work done was $mgh$!" Well, it is, if you only consider the work you did to lift the box. This is what you would measure if you used a crane to lift the box, for example: the amount of work that needs to be done by the crane is $mgh$. However, gravity did the opposite amount of work, which canceled out the work you did (except for those brief moments at the beginning and the end, but those two contributions cancel each other out anyway). So the total work done by all forces involved is zero.
This might seem a little confusing - perhaps you're wondering, if the total work done is zero, how did the gravitational potential energy increase from $0$ to $mgh$? The trick there is that the "work done by gravity" $W_g$ is actually the gravitational potential energy under a different name. For conservative forces, we define $\Delta U_i = -W_i$: the change in a certain kind of potential energy is the negative of the work done by the force corresponding to that potential energy.
In this case, the gravitational force does work $-mgh$, so the change in gravitational potential energy should be $mgh$. But once you start calling it a change in gravitational potential energy, you can no longer call it a contribution to the work - and that leaves you with just the $W_\text{lift} = mgh$ contribution. So in that case, if you label the "action" of gravity as a change in potential energy rather than a work, the work done is $mgh$.