The safest way to verify a patched ROM is by its checksum. A clean ROM has a specific SHA-1. A "patched up" version for AP will have a different hash. Use a tool like ROMnalyzer or consult rom-hacking forums for the specific hash of the latest v1.1 AP patch.

Which of those would you like?

If you're patching to get the "complete" experience, remember the DS version natively includes: Chrono Trigger DS Anti-Piracy Patch - RomUlation