After the Tomb where do I go? Do I go to the underwater place? If so where is it? Also how do you become an assassin? And is having all ninjas bad?

It is best to complete as many of the guild quests (these raise your GUILD LEVEL which can be viewed in your journal) as possible before heading to Ishad N'ha. I think you can tell when you are maxxed out because each Guild Master will say, "I have nothing for you now."

To become an Assassin you need to find Scanthril. He's a ratling who hangs around the burnt out building between Ishad N'ha and Dragonspire. He will give you two quests (1) Find a dead stout called Grundel(sp?), he's the corpse next to the writ for the stout mines, (2) then he will ask you to kill Raskallion, he's the stout who's hiding from Freyedies in the depths of the stout mine. Only then will Scanthril give you the Assassin's Dagger (looks like a Skull Dagger), next time you go into a pawn shop you get the opportunity to promote whoever is holding the dagger to Assassin. Note that if you say no to the offer that character will not get asked again. Also killing Scantril will only get you an ordinary dagger.