To use your email signature when replying to an email, do the the following:

1) Hit the reply button in Apple Mail
2) Exit Apple Mail by using the Menu button (the hardware button at the bottom of your iPhone)
3) Run the Email Signature app, and select your signature
4) Your selected signature will be inserted into the reply email
5) Compose and send the email as normal

Note: follow the same procedure to forward an email.

This process is required due to the limitations that Apple applies to ALL Third Party applications, Email Signature Pro included.