i'm installing new msd 6m2l boxes to replace my factory merc igntion system, however i still want to use my factory distributor. In the diagram they show to still use the igntion amplifier? is this my thunderbolt module?

I think thats what they mean. You still need the ignition module with an MSD box if you use the TB IV distributor. There is no timing advance in the box. If you used an MSD distributor, the timing curve is in the distributor.