Sorry for the double post but it will not let me edit my post again.
I got it to work and here is how.
1. Set Up the first filter
a. Use the main setting you want to use to reply back, if it's all email coming in just us "To" "is" "youremail"
b. Set a negative related to the second filter. For example "subject" "does not contain" "Re:"
2. Set up second filter
a. Condition one which is the opposite of the negative of filter one. "subject" "contains" "Re:"
Won't work perfect without some testing and do not use "subject" "starts with" "Re:" That is what caused my last test to fail but figured it out.
This will get you two levels of replies and if you really wanted to get crazy you could get beyond that just by using negative filters but it would require a lot of testing and using different subject for each email so you could use "subject" "contains" "Re

name of email)"
Hope this helps you out.
Once again sorry for the double post.