ACE is a virtual synthesizer, it doesn't read MODs at all.
You can add samples to it but they're only as "additional help" because normally all sounds are generated in real-time there.
You can contact authors about format of the samples (here You can find their addresses: http://nb.atari.org/main.php?page=contactus
), however I am not sure if they can help because a year or 2 ago, I was asking them about sample-format of their FlexTrax editor (whether 8bit only, or maybe also 16bit samples in extended FLX mode?) and the guy answered he doesn't remember, after years.
Anyway I wish You luck and I hope You will upload Your ACE songs if they're ready.