Where it applies. But the President may not enforce the laws where they do not apply. When the south seceeded, the laws of the United States did not apply to them. Before you can say the laws should apply, you must explain why the south had no right to seceed.
If you wish to say the states had no right to seceed, you need to explain why the Declaration of Independence is wrong.
As a hypothetical question, suppose secession was legitimate. Now, which branch or officer of the federal government would officially "certify" or notice this fact? Is the President supposed to be the one to decide? What if there is dispute in the "seceeding" state about the legitimacy of the action -- say, if a strong minority opposing secession claims the vote or convention was rigged -- is the President the judge of this? The Congress?
The question of the President's authority to determine that a state has left the Union is not a trivial one. It is difficult for me to understand how one can defend the claim that the President of the United States is supposed to abandon his oath to enforce federal law as soon as he decides that a state convention or referendum, having no explicit Constitutional standing at all, informs him that he should. It seems to me that at the very least he should await the confirmation of the Congress, as in the admission of new states. But that, at least, is a procedure which is defined in the Constitution.
Overall, it seems to me quite Constitutionally daring to suggest that the President can, on his own authority, recognize a secession without the Congress certifying it. But, of course, Congressional "certification" of secession is quite close to federal approval of secession. So I wonder what account secessionists give of how, actually, the federal government is intended by the Constitution to officially "notice" a secession?
In the absence of a clear answer to this question, it seems to me that the President had better keep enforcing federal law -- that, at least, is certainly his job.