Good day @mydrone, so sorry for leaving you hanging.
If you simply want to override the pwm output you could take a look at an example in our docs which should be of help.
Are you talking about creating your own controller as in RC controller or using a keyboard to control the drone? If so, the code above should point you in the right direction, as it shows you the whole (code-wise) process once you already know which values you want.
At first I though you were talking about creating your own autopilot software, which surprised me.
For further modifications of the ardupilot software I'd personally go to the ardupilot forums (their servers are having problems when I'm writing this) and/or DIYdrones, there will be more knowledgeable people discussing things that could be of interest to you.
Also, I know we've been slow to give support on the forum lately (we returned from vacation this week) and apologize for it, but I'd ask you to please refrain from creating multiple posts, reopening old ones and even creating a different account to do the same. We are working our way through the forum and spamming doesn't help you or us.