I'm using this migrator tool and so far have had no problems at all. It creates a dummy FSX install, which is enabled and disabled as required. Read the manual about when you should have it enabled or disabled. I'll say that again... read the manual about when you should have it enabled or disabled.
I've installed the following with it, and so far have found no issues:
Aerosoft's Beaver X
Aerosoft's Catalina
Iris' Vulcan
Tongass Fjords
Do NOT, however, use it with any Orbx FTX scenery that only has an FSX installer for it. Install FTX-for-FSX scenery into Microsoft FSX as you would normally, and then use Orbx' own FSX/P3D migrator tool. Of course, if you have Orbx scenery that has a P3D installer, then that can go directly into P3D ( they are gradually rolling out P3D installers for all their downloads, but it will take time ). Once that is done, install the latest Orbx libraries directly into P3D using the P3D installer that comes with it. The libraries must go directly into P3D - they wont transfer from Microsoft FSX.
Anyway, so far the Estonian migrator has made P3D add-ons painless and is probably the most essential tool you can have if you are moving over to the new simulator. Just make sure you read the manual about when you should have it enabled or disabled.