The version that is loaded by Apache is determined by the version that is seen by Apache, i.e. the one that is dumped in the Apache modules directory. If your installed version does not overwrite the one in that directory (presumably installed from the package tree), the distribution's version will be served.

Whether you can use your compiled version depends on whether your compile process has created a libphp5.so. If there is one, you can then try to overwrite and see if it works.

If you compile PHP as CLI or CGI, then you will not get that shared library. Then you will need to recompile your PHP. For details, please check the PHP manual for compilation hints.