so i want my assassin to be in a relationship with her padawan, but since we don't know when that will be happening my question is this: Can you go through the whole story of an assassin and not do the relationship stuff BUT come back to it even after the story or is it directly intertwined with the story?

The romances are part of the companion storyline, and have nothing to do with your class story arc. I have no idea about going back to a romance after you've progressed past it in the companion arc though.

To the best of my knowledge, you can always just delay/refuse to start companion conversations, and thereby save the relationship stuff for later. Companion conversations sometimes don't start until after a certain plot point, but you're never obligated to complete a conversation before some chosen plot point.

 

However, you can't do her regular conversation line while saving the romance for later. It's all or nothing.