Kinga,

If you're referring to the confirmation email that is sent out when a candidate applies, that can be changed in the Website tab -> Customize Email Messages location.

If you're talking about the message that appears on your careers page, then you would have to do a couple things:

1) Make sure your Custom template is enabled by going to the Website tab -> Page Design -> Click the Custom option and the Save button.
2) Then, click on the Custom button and click OnApply.html. You'll see a message there that you can change to your liking.

I hope this answers your question!