if you would like to get flange stresses and interested in bolted area, you have to either use tying to give same displacement b.c. to both flanges at bolt points or model even bolt. If you are not interested in flanges but in far area than just use tying or even you can combine those nodes where the bolts are. Which program are you using?
Motor rotates the first flange and there is resitance at the other end. So, you can fix nodes where motor/shaft is connected to flange and apply torque to other end.
If angular velocity is also of concern than you should include in this static analysis the angular velocity b.c. which you enter only center of rotation, density of material, velocity.

hai netjack,
Thank you foryour reply,I am using Ansys.I am interseted in stresses at Bolts,Being they are in rotation , i am in confusion to give the DOF,
Thank you again