yeah, this is all basically correct.
as for your questions -
1 - you just need to extend either BaseEPEncounterCreator or AbyssalRogueStellarObjectEPEC & override the getFrequencyForPoint() method, you can then have that return whatever value you'd like
1b - adding a new manager will probably be a bad idea, but just adding your creator to the CREATORS list should work fine.
2 - you can do this with your mod's modPlugin & it's various methods - if you want to go with multiple discrete creators for each encounter I'd use onGameLoad(), that gets called after the save has been loaded & will allow you to only add the encounters that haven't already been seen (though might cause some wierdness with loading saves after the encounters have already been added? could probably just brute force past that by removing them all before adding them again?).
Alternatively, you could have a single creator that gets added to the list in onApplicationLoad() (which gets called once when the game launches), then have that do the checking for what encounters should be allowed to spawn when the player is actually in-game.
hopefully my ramblings make sense