If someone has
done you a favour and you tell them that you don'
t know how to thank them, they could say: "You can thank me later" in the sense of that you can do them a favour later and
help them with something.
If someone does you a favour and you don't thank them for it and don't seem grateful, they
may say in a joking or
sarcastic way: "You can thank me later" as a gentle or subtle (even unsubtle) reminder that you should be grateful to them.
If someone gives you a word of warning or tips to avoid you getting into a crisis and you think the advice is unnecessary, they might say: "You can thank me later" or "you'll thank me later" in the sense that although you don't take their words/actions seriously now you'll eventually realise that they were right and
will be grateful to them - even if you'
re not grateful now.