Get the sources you want. Like the frontpage extensions, phtml includes a security problem because it is run under the uid of the webserver. There are some other options in php.h you may want to edit. If you are very concerned about security, compile php as a cgi. However, this will be a performance loss and not as smart as the module version.
Type make to build all files.
You may also want to add index.phtml to DirectoryIndex in that file so that a file index.phtml is automatically loaded when its directory is requested. You may issue make test to verify the compilation. You have to apply a patch to apache. It is important that you apply it before the frontpage patch, otherwise frontpage will not work. You now have to apply the FP patch.