Having worked with Waters Empower 3 for 10 years, I can tell you it really depends on what aspect of the software you use the most. You could pick up the running of samples, making sample sets and instrument/processing methods in a few months. It takes maybe about a year of making sample sets and running samples etc to get up to speed. As with everything, its only when things go run in the methods/sample sets that you gain valuable experience!
However, you may never need to create custom fields, nodes, systems or users, so these functions may be alien to you. Its usually an administrator who sets policies and creates users so this part of the software may not be relevant to you. I know in my case, I was using it 7 years before I knew anything about calibration curves and how Empower generates and stores them so it really depends on your own usage of it.
If it helps, there are dozens of online courses offered by Waters which explain everything from the processing method to custom fields, login and data acquisition, and they are all very helpful.