You can certainly do all that, and it would undoubtedly be educational to do on a couple of rockets. Usually, though, it's more than you need.
You still haven't provided your original ORK file that was "way off" on the mass estimate, so we don't know what specifically caused your problem with that file. But generally, if you specify the parts and materials correctly in OR, the mass estimate for the whole rocket will be pretty close. Generally it will be a little low, and the CG will be a little farther back than predicted, due to the preponderance of glue being applied in the back of the rocket.
Again, there's absolutely nothing wrong with weighing every part as you assemble and overriding... but I don't usually do that, unless it's looking like stability is going to be borderline, or if the mass is coming up on the high end of what my motor mount can support.
No matter what approach you take while building, when you're done you absolutely must weigh the rocket and measure CG, and override them in whatever fashion you prefer (use the global overrides, or add mass elements and position them appropriately). When making the final determination of rocket stability and getting flight sim info, the only thing that matters is the mass and CG as-constructed.