(Abridged) We use 95, 150, and 220GHz observations from the SPT to examine the SZE signatures of a sample of 46 X-ray selected groups and clusters drawn from ~6 deg^2 of the XMM-BCS. These systems extend to redshift z=1.02, have characteristic masses ~3x lower than clusters detected directly in the SPT data and probe the SZE signal to the lowest X-ray luminosities (>10^42 erg s^-1) yet. We develop an analysis tool that combines the SZE information for the full ensemble of X-ray-selected clusters. Using X-ray luminosity as a mass proxy, we extract selection-bias corrected constraints on the SZE significance- and Y_500-mass relations. The SZE significance- mass relation is in good agreement with an extrapolation of the relation obtained from high mass clusters. However, the fit to the Y_500-mass relation at low masses, while in good agreement with the extrapolation from high mass SPT clusters, is in tension at 2.8 sigma with the constraints from the Planck sample. We examine the tension with the Planck relation, discussing sample differences and biases that could contribute. We also present an analysis of the radio galaxy point source population in this ensemble of X-ray selected systems. We find 18 of our systems have 843 MHz SUMSS sources within 2 arcmin of the X-ray centre, and three of these are also detected at significance >4 by SPT. Of these three, two are associated with the group brightest cluster galaxies, and the third is likely an unassociated quasar candidate. We examine the impact of these point sources on our SZE scaling relation analyses and find no evidence of biases. We also examine the impact of dusty galaxies using constraints from the 220 GHz data. The stacked sample provides 2.8$sigma$ significant evidence of dusty galaxy flux, which would correspond to an average underestimate of the SPT Y_500 signal that is (17+-9) per cent in this sample of low mass systems.
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