When calculating the lift coefficient,should I use only the lift provided by wings, or also the net upward forces of the entire aircraft?
If you want the lift for the whole airplane, of course you add the contributions for each part. While the fuselage might indeed contribute a positive lift, its presence will lower the lift of the wing. In the end, all parts of the aircraft will stick together when it flies and need to create just enough lift to keep its mass airborne, so it makes sense to look at the sum of all parts.

Since the wing will dominate lift, it is common for first-order calculations to consider the wing only. However, if you have data for all parts, you should include all their contributions, too, for a more precise result.