You definitely can use as many Mandalas as you want with Battery 3.
At the top of Control Burst you 'Assign a Channel' for the Mandala you
are bursting. Make each Mandala a different channel and they won't
overlap at all in Battery. Just make your Battery cells look for
individual channels instead of 'Omni'. You could also download
Control Burst EXP from this forum and really go nuts by setting every
zone of every pad to different notes and channels. That's all up to
what you want though.