TSRemux is not needed if you use TSMuxer. TSMuxer is much more advanced IMO and is quite easy to use. The "trick" on seamless branching titles is to find the right playlist. For that you'll need to go through them with BDEdit to find the one that matches the main movie. A little trick someone told me is to look for the larger playlist files on the BD itself and check those first. One of them is bound to be the movie. Open that playlist in TSMuxer, set the output to BD folder structure, and it'll create you a folder that can be converted to ISO and/or burned. Or output it to m2ts and you can then split it for multiple DVD's as this guide was originally showing.

The reason this is confusing is that it's new technology and the tools aren't really developed to a "point and click" type of polish. If that's what you're looking for, you're going to be sorely disappointed. We're a ways away from that point. We're getting closer with each new release of these tools but we still have a ways to go. BD structures are enormously complex.