I believe he says 'Do you want to go to the roof with me?' or 'do you want to go up with me?'
The end of the film is supposed to indicate that Theodore has overcome the crippling insecurities that were stimulated by the failure of his relationship with Catherine.
Samantha has allowed him to recognize that he and Amy are a good match, and would probably prosper in a relationship. His asking her to go to the roof with him is a proactive action on his part, and possibly foreshadowing him asking her to be in a relationship with him. Her agreeing to do so is indicative of her accepting this proposalreciprocating interest in him, and saying yes.
The separation between Samantha and Theodore is, whilst unrequited, amicable and necessary, and seems to have allowed Theodore to re-evaluate his attitude towards love. He is re-inspired;.