Cobrahistorian,
A lot of the force distribution is set by the CENTCOM AOR Commander and his staff. There are a myriad of things they look at to include assets available in the AOR, capabilities of the assets, and the mission requirement. Troop rotations and the needs of the Services also come into play. Lately, the priority has been Iraq. The Marines even had CH-53Ds in Iraq flying with the 31st MEU (SOC)! For a while there, the USMC Cobra and Huey squadron were Reservists with the CH-53E squadron being an Active Duty one. Since then, the 53 squadron has rotated home.
As for the CH-46E, it's not as good as the CH-47D at higher altitudes so that's why you see the MEU operating more down south in Afghaniland. On a side note, every USMC CH-46E squadron has deployed to the CENTCOM AOR for OEF/OIF at least once except for one Active Duty squadron. This rotation has also included USMC Reserve CH-46Es as well.
The Marines being transported around Afghanistan in Army CH-47s is a good example of how the Joint World is working well. I've even read of instances back during Vietnam where Marine Recon Units worked so well with Army aviation units (flying UH-1Hs) that the Marines actually
preferred the Army flyers to get them out of a "hot spot" vice a Marine CH-46. Just goes to show the comraderie that can build between fighting men. We banter back and forth between the Services, but when the rubber meets the road, we're all one Team.
Okay, I've rambled on enough...hope I answered your question...