We normally use 1x2x3 or 2x4x6 blocks with a clamp on top. As a programmer, I will import the setup CAD models with the part model into MasterCam and place them how I want then save the setup CAD only and import it into DMIS so I can program around it.
We also ordered some vacuum cups and related hardware recently so I am in the process of modifying programs to use that as well. No all programs but the ones that I deem it acceptable to use it on. Setup is much faster and more versatile with the vacuum.