I have tried to research this because I know it can be done. I am registered as the Scoutmaster in my troop, and also registered as a roundtable staff member, but one is a troop level and one is a district level.
I found this in the Guide to Safe Scouting, page 7:
A unit leader may not serve simultaniously in any other position within the same unit.
Then it refers you to the Rules and Regulations of the BSA.
I think they mean that a Scoutmaster cannot also be registered as the Cubmaster.
In the situation that dparker mentioned, if you are combining two sperate scout groups that are also chartered seperate from one another, I dont think it is neccessary to register under both charters.
Have the SM from each group work in tandem or select one to be over the two groups.
When you have awards to be presented each group will have to record there awards seperate from the others, and each chartered group will have to keep there own set of paper work.
I see this alot where I live in Utah. My unit is sponsored by the Church of Jesus Christ of Latter-Day Saints (LDS or Mormon Church) the geographic area of each congregation or ward is not very big and it is not unusual to have a small Troop to work with. I currently have 9 scouts including the new scout patrol. I see units combine alot for meetings or campouts.