Im a full time flight attendant and travel with work more than 50% of each month.

Id like to buy a duplex out of state, using an FHA loan, and occupy one of the units for the first year.

I currently rent a room in NYC and would like to keep it for layover purposes, while the new property (in SC) serves as my primary residence.

How often must I be physically present at the duplex, for it to qualify as my primary residence? Will I get accused of mortgage fraud if my job causes me to be away much of the time? 

The eventual goal would be to rent out both units, but I need the FHA to be able to afford the down payment on the property.

 Newbie here! Any and all advice is welcome! 

you have to live there the "majority" of the time... and it's based more on intent then anything else.

There is not a defined percentage of time you must occupy the residence so long as it is your primary residence and is used as such (you get your mail there, your license has that address, etc). Long-haul drivers and salespeople also travel a lot for work and can be gone weeks at a time as well so you shouldn't have a problem in that regard. No one from FHA will come and knock on your door to verify you're there a certain amount of time so just be honest with the application and it things should be fine.