Don't get a LOR from a teacher you withdrew from for the reasons you had to withdraw. If the reasons weren't that you were doing poorly, that would be one thing. But if he or she is giving an honest idea of what they've seen from you it's that you had to see the material more often and longer than other students and they know that you did poorly on initial tests and quizzes. Just a bad idea.
W's in general, in my n=1 experience, are overblown as costly on sdn. However, W's in multiple prereqs, and W's in the same prereq twice would be a red flag. I think you need to stack some upper level bios with solid grades and no W's on top of your two W's to show it isn't an area of weakness. Also, in the interview you should be more creative then that you didn't do well on an early assignment. I'm not saying to lie, but if the question isn't asked incredibly directly, then try to word it in a way that speaks less about you not wanting to tank your app.