I’m not the right person to answer your question, hopefully one of the abinitio people will come along and take a look.
If you can afford the time, run with relax. If you can’t afford the computer time, then run relax on the best of the results instead.
Determining the most probable structure from thousands of results is based on two things: clustering, and the score. If you find that many, many models cluster into one group, and several of those models have better scores than other clusters’ best members, then Rosetta thinks that’s how the protein folds. If you get no clear clusters, or no score discrimination between clusters, then Rosetta doesn’t have a solid prediction.
Validation of these structures is an entire field in itself. You have to decide based on your system what you want to do to validate. The most obvious thing is making point mutations of buried interactions in the protein. If your mutation would destroy a predicted interaction, and the protein unfolds, then it’s consistent with the structure. If the mutation doesn’t stop folding, then the prediction is wrong. Experiments in this vein can get endlessly complex.