Dave, let's see... Raw water pump goes: thru hull, strainer, raw water pump, HX, exhaust riser nipple, muffler and then out the transom.
You don't want to (over) fill the muffler, so the separate pump should only come on when the engine starts, not before.
That seems to leave out the ignition switch, 'cuz the switch needs to be on for quite some time before the engine kicks over: glow plugs for anywhere from 12 to 30 seconds. You don't want to fill up the muffler by essentially "cranking" for that long 'specially if you have to actually try starting the engine more than once.
Your alternator? Hmmm, let's see: There are two possible alternator output wiring shchemes that folks have on their boats.
1) Alternator wired directly to house bank: will always be ON because of the connection to the house bank and its negative ground (whether separate or case-grounded through the bracket) - that circuit would always be powered (have power "there") if you connected anything to it (the alternator output)
2) Through the C post of 1-2-B switch: same thing when you turn the switch ON.
Conceptually, you want to have that pump run ONLY when the engine is going.
Since heat doesn't build up immediately when the engine starts, a short delay between start and pump run can be accommodated.
One item already exists for this: the oil pressure sensor.
Consider using that as your "built-in" relay. Parallel that to your pump circuit.
Only other thing I can think of is a manual switch in the cockpit, or do it down below and just hop down when the engine starts and stops.
Good luck.