What you are describing is why the fluid power industry has been advocating getting away from NPT threads because they are difficult to install properly and they are prone to leak - especially if not assembled properly.
That being said - the IFPS stance is to not recommend NPT fittings but if you have no choice then it is important to install properly. We don't recommend a procedure since we don't advocate their use. I would sugggest that you rely on manufacturers guidelines. Here are some important guidelines:
Do not overtighten: Overtightening can damage the threads and cause leaks. This is extremely important as you can easily damage threads or crack the port. It is important to understand that torque is not the appropriate assembly technique for NPT assembly, but rather thread engagement by the number of turns. Torque is not an appropriate method to makeup connections due to the differences in thread surface roughness, variance in threads and taper, lubricity of thread compounds, and other factors.
Select the correct size: Ensure the fitting size matches the pipe size.
Use appropriate sealant: Choose the right type of thread sealant based on the application and fluid being used. Ensure no sealant on first two threads.
For additional info, I would suggest that you look to specific manufacturers guidelines as they are the authority.