I normally backup with Timemachine having the HDD directly connected to my computer. Now I want it to backup over Wifi using my Airport, but it does not recognize the old backup when doing so. Any tips ?
It uses a different storage format, so you can't just plug it in to the airport and resume backups. It is easiest to just start over. If you REALLY want to keep using the same backup there is a process here you can use to do that.
Also, what version of the Airport are you using? On models older than the current tower version backup up with Time Machine to a USB drive attached to the Airport is not supported by Apple. It is supported on the new tower model though.
Also be warned the the first backup over wifi to the the extreme can take a very long time. It has to do a full backup. Best to do the initial backup over Ethernet.