Having some sort of prompt that leads them to S4vant is a good call I think, but in terms of when the first reset happens, I would have it happen organically. From just reading it, the Apotheosis Engine seems to cover its bases well so I would let it do its thing: If the defeat a myth, that triggers the first reset aand they will reset to where every they were when that happened. If they are going to be killed, the reset triggers and they respawn thier for the rest of the adventure. If someone else is going to be killed, where ever they are when that happens becomes their reset point.
It could get a little complicated so maybe having some guidance on it for the GM on the first loop would be good. Its extra but you could also have a little check box beside each location for the GM to physically fill out when they set it as a reminder.
Does that make sense? It is totally possible I am missing something