Really I have to agree with Kerry, BD Rebuilder once everything is installed and a few adjustments in ffdshow and use the inspect exe. to make sure everything is setup correctly, it is clear sailing after that.
And the program is easy to use and will do just about anything one would want to do IRT blu-ray.
Even though BDtoAVChD can compress, I never use it for that.
I mainly use the program to remux main movie only, sometimes downgrading the audio if I can make main movie fit on a disc.
I believe BD Rebuilder can encode faster therefore I use it for compressing to Blu-ray disc.
This is just my method, likely you will find most of us don't re-encode as much nowadays and simply prepare blu-ray files to store on hard drive.
So from what info you gave us, if I were in your situation, I would try out BD Rebuilder, I don't think you will be disappointed.
Kerry can help you out along the way as he already mentioned.
And you can use BDtoAVCHD for remuxing for movies that will fit without the need for re-encoding, I really like the program myself.
It won't hurt to fool around with these 2 programs and see how they work.