Installing an Eaton CHSPT2ULTRA Type-2 surge protector
You'll need to use the 50A breaker, and you can cap off the spare hots in the panel
The bad news (not that bad) is that in order to meet the listing and installation requirements of the CHSPT2ULTRA, you're limited to a maximum of a 50A breaker for it.  (You can install it on lower-rated breakers, but they might trip during severe surge events, taking the surge suppressor out of the picture.)
As to the spare wires, simply capping the unused hots off with wirenuts and tucking them into an out-of-the-way corner of the panel is the best approach.  That way, they are terminated in a place that someone who wants to use them later can actually find them, as opposed to having to go on a scavenger hunt for the loose end, and you don't need to stuff an extra junction box in by the panel for the termination either.