As Gary had said, to 'Check on you" means that either someone is making sure your doing okay, or if you need any help, or making sure you're not doing anything wrong. If "Check in you" is supposed to have a similar meaning, it could actually be "check in on you" which is really the same this as "Check on you". If it is supposed to be in reference to something like a registering for a hotel, or at an airline ticket counter, then the phrase might be "check you in".

Check in means- Go to look in (on someone or something).

check on someone means that you are watching them, making sure they need something, or watching that this person does not do something inappropriate or suitable to the situation. I don't think check in someone means something. However, when you check in at a hotel, it means you are registering to stay at the hotel for the night or for many days. Check in something also means that you are registering a thing at someone's place as a return, for example.