In the US I believe a Check is the same as a Cheque in the UK. Granted cheque is a homophone but both usages denote money (more so with the US title) with the added benefit of the connotation of arriving at a hotel. I am a big fan of puns.
When you check-in to a hotel you aren't "handing over a cheque", you are checking-in with the reception. Ie., you are speaking to reception and checking your reservation/room.
To "check in with someone" is to have a chat or talk to a person to "check" how they are.