It doesn't matter whether CA Top Secret is started before CAS9 or after.
If you start CA Top Secret first, you will get messages saying LMP key required every 30 seconds until CAS9 is started. This message won't stop anything.
If you start CAS9 first, you should code the following in the CARIMPRM member:
PRODUCT(CAIRIM) VERSION(S910) INIT(S910INIT) PARM(SSF(TSS))
to avoid being prompted to enter the security package.
CA Top Secret has an AUTOCMDS DD statement that points to a dataset that can be used to start applications after CA Top Secret has finished coming up. CAS9 could be started from here if you want to start CA Top Secret first. Or you could start CAS9 first from SYS1.PARMLIB(COMMNDxx).