I would have expected someone much more knowledgeable to chime in about this by now, and was interested in seeing what they offered. But since so far all we're hearing is crickets, herewith my guess. Don't take it as authoritative, though:
The TSS JCL specifies, among other things, the DSN for the Audit file. So I suppose you could easily enough do this:
1) Copy the current Audit file to each partition, giving it the proper DSN.
2) Copy the current JCL for the Top-Secret STC to each partition.
3) In each partition, modify the JCL so that the Audit file points to the appropriate "local" DS.
I gather you want the other TSS datasets to be shared, as before, so I guess you're sharing DASD across the partitions (or at least some HLQs. If so, maybe this is all that's required? But I'm not a systems programmer (I came into security from the developer side), so there's lots I don't know.
By the way, you say "audit file" and I have to assume you know what you're talking about. But I'll mention in passing that I occasionally confuse the audit file and the recovery file. I forget, does the DD name for the audit file include the word "recovery", or does the recovery DD go by "AUDIT"? Something like that, anyway. It's been a while since I had to look at it, but as I recall the audit file records security violations, and the recovery file records TSS commands (so that you can look back at what commands were recently issued and have a hope of ~recovering~ the system from a disastrous mistake).