I didn't want to flood DMP with questions, but based on what you're saying, this is what you did:
1. Set the time and started first timer.
2. Started game when the first timer's first countdown ended.
3. Entered the game, checked to see if you hit Timer0 via Chatot. If you did, then you turned on C-gear.
4. Hit the Entralink button, waited in the "x entered the Entralink!" till first timer's second countdown ended. At this point, when you press A, you started second timer.
5. Advanced IV frame (if necessary), talked to target Poke, waited till second timer ended before battling Poke.
Am I correct?