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.
from saturday night live's hans and franz 'pump you up' guys
the idea that a 'truth' might currently be being dispensed, but YOU are too preoccupied, (or too "smart") to absorb it at this particular 'juncture'. you MAY (or may not!) be able to view it from another position sometime in the future, in a different light. (anti-'pot' people??, 'case-hardened' conservatives??)
this life is a double-edged sword!! alcohol isn't that great on the frustration/s!! pass me that gage and hear me now, believe me later!! -i need my "medicinal" marijuana!!
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.