justin,
I know exactly where you are coming from! The fist time I had to remove the BB I deliberated for a good few minutes as to whether it was better to put the EBB in a vice or to simply leave the EBB in in the frame.
Between the two thorns I own, I have now removed a bottom bracket from an EBB 3 times. I don't know if there is a proper method but, each time I have done it with the EBB in the frame. (Make sure that the EBB bolts are secure!)
Best of luck
Stutho