Sounds like you have two build trees you can't tell apart. However, Apache installs to one location, so you should only have one installed, just two directories you built from. Correct? Perhaps you can look at the complied files and compare them to the installed files.
A simpler way is to use the httpd packages like foolish suggested. Install httpd-devel by running
yum install httpd-devel
It has apxs. DSO (mod_so) support is already in the rpm version.