I have also used IonCube. I found the whole process fairly simple. From creating an account on their website, to downloading and installing the software, and buying a license was all quite straight-forward and painless.
Using the application is simple too. You can tell it which files to encode, and you can even have it put a comment header in each encoded file so you can put something like "This file is encoded to protect the copyright. Please contact My Company for questions... etc." A nice things is that it does not have feature bloat- it does what it says plus a few nice-to-have features, with no unnecessary complexity.
The IonCube encoder can also obfuscate non-PHP files like Javascript files for you too. You can tell it to put the encoded files in a new folder by themselves or copy the other non-modified files along with it too, so you are kind of doing a 'build' of the project. I found that it was a great deal and I am able to continue using it without having to pay for a new license unless I want it on another computer or want a new version. So I've only paid once and used it for 3 years now.
A couple drawbacks of encoders in general. 1- you can no longer edit files 'on the server' which while that's a bad thing to do anyway, it prevents you from doing emergency fixes if you don't have access to your computer (like if you are on vacation).
Second, if you modify the project and add new files to be encoded, etc... you must update the IonCube project's settings to include the new files that need to be encoded. I guess I just find the added step a bit annoying- but worth it if you need to protect your code AND give your users FTP access.
You can also use this encoder regardless of which IDE you use, because it is a stand-alone app.
I agree with some other posts that encoding is not a perfect solution and in some ways goes against some people's feelings... but for myself it provides piece of mind.