Modify the atari800 package script and replace the URL to download with your own URL to the new version. Make sure that it's not a 'redirect' or 'wait x seconds to download` and it's a direct link. After you replace the URL, use RetroPie-Setup to install from source the emulator.
@meleu I use emulated arm chroot with qemu on x86_64 pc with ubuntu, but also cross compiler on the host via distcc. (I don't have time to do any write up but there are some on the net).