The holy water isn't for the guy in the green house. It's for someone else in the Hand, I'll let you find.... her. You'll find the "pure" water needed in the Dorn's Deep area, with the giants. The tomb of which you speak is supposed to contain a rift into the negative material plane. That's where the undead are coming from, so of course they can enter the tomb whenever they wish. The liches phylactery (??) contains his "life force" which doesn't like the negative material plane. You're supposed to formally introduce the two in order to wave bye-bye to the liche. We'll need more info about that other problem (never recognized?) before we can enlighten you. Don't get too frustrated with the game. Most of the stuff that's tripping you up are just minor quests not needed to complete the game. For the main quests, just make sure you pay attention to what the NPCs tell you and you should be all right.
Good luck!
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