they don't need to be engaging in negotiation on this, or submitting it to the court.
act as a co-equal branch, exert this power - and if the other two branches want to do anything to thwart that, let them act on their own to do whatever they want. if congress wants to impeach the president over this, let them make that move. if the courts want to stop it, let them make that move.
and all the while, the president needs to be making the case to the american people about what actions are needed in the war on terror - so when/if the other branches act to undermine that, the people can see it and vote on whether they agree with it or not.
One of the things not mentioned is the probability that after it's submitted the FISA court may even rule that they don't want to be involved in a battle between the executive and legislative branch.