So when there is a quest active, I get that missile shaped marker on the map to show me where to go, but for some reason, in addition to that, I'm getting another marker in addition to that. It's transparent, so it has the same shape as the regular quest marker, but it's transparent, with the missile shaped outline. I can't figure out what this signifies.

Its your own personal "quest maker," on the map in your pip boy you can set it to be anywhere you want so you can help get yourself from place to place.

Ah!! Thanks

Look in the "Vault Dweller's Survival Guide", the game manual, if you have it.
Might help tell you about the other markers.