That's really not true. The President doesn't swear under oath to obey Congress; he swears to preserve, protect and defend the Constitution.
If there's a constitutional question that hasn't been addressed by the Court, the President doesn't just sit around twiddling his thumbs wondering what to do. Nor does he go to the Court for an advisory opinion before he can act. He gets his army of lawyers to answer the Constitutional question for him, and then he proceeds accordingly. After that, it takes months or years before an actual case addressing the question gets before the Court, at which point the Court will finally decide whether the President's determination was right or wrong.
Well, the fourth amendment is pretty clear. FISA does not limit the President - it actually broadens his power to obtain warrants - in this case, secretly.