Author Opinions Needed

I received my first two personal notes on rejection letters from agents that I had queried. I feel like it is a small victory. Now the question is how do I use those personal messages? One said that they weren't sure what to do with a self published novel as opposed to one that was yet unpublished. But she praised the story as creative and well written. I thought when I finish my next novel, she would be one of the first agents I would query with a "Hey do you remember me...". The other note was on the novel that I am currently writing. The agent said the story had tons of potential but they felt it needed more work before it is sent out as a query. I agree with that statement wholeheartedly since the novel is not finished. I am going to add this agent to query when it is completed. Any other advice on how to use personal comments to enhance a query letter?