Welcome to the forums dhnj.
To combine DVD's into a Blu-ray using BD Rebuilder, the first step is to put all of the DVD's into one folder. This means you would have a top folder, lets call it DVD Input. Inside this folder would be all the individual folders of your DVD videos.
For example, I want to combine all four of the Jason Bourne movies. I'd have this DVD Input folder, and within it would be four movie folders named The Bourne Identity, The Bourne Supremacy, The Bourne Ultimatum and The Bourne Legacy.
Ok, next step is to change the Mode in BD Rebuilder to Quick Play.
Next, click on File-->Import-->DVD's (Quick Authored) and select the DVD Import folder you have set up.
Let the program process all of the input files, create faux Blu-ray structure and convert the audio. Once it is done with that, click Backup to start re-encoding the video.
Default output size is for a 25gb disc. I've never tried to put more than four DVD's on this size disc.