I want to keep all same - confirmation page, email notification page. But I want to add attachment with the email. I have created an own php app which transfers data to my excel file and then it is sent by email. It is working well along.

How can I add this new excel file (sometimes I create pdf file with php) in default email?

When working with data in php that may be used for excel I always convert to csv.

Generally I transfer data to pdf sometimes excel used and send by email with php app.
My target is that I want use coffeecup notification email with attachment. So where should I edit so that I can call my php app and then send email notification?

I always write my own myformname.php to handle custom processes. I would think you could handle it on the existing one but it will take some testing to see that everything works properly.