PKJENNY,
The calculation will depend on the purpose of the analysis. You haven't told us that. The ATS has a fault withstand rating based on current through the ATS. This assumes the current is coming from one source or the other. So just take the worst case if you are interested in determining if the ATS has an adequate short circuit rating. Even if both sources are energized, the fault current through the ATS will be coming from one source or the other, not both.
If the fault is INTERNAL to the ATS, AND both sources are energized, then the fault current will be the sum of the two sources, assuming they are in sync. But what is the purpose of this calculation? Perhaps an arc-flash calculation for the ATS if you assume both sources will contribute to the fault. If the two sources are not in synch, then the calculation is much more difficult and depends on your assumption about relative phase angles.
Good luck,
Dave