Only 2.3% of extra heat is warming the atmosphere, so the recent slowdown in atmospheric temperature increase is just temporary
Where is global warming going
Only about 2.3% of the excess energy is used to warm the atmosphere, while about 1.3% is used to melt glaciers and about 0.8% is used to melt Arctic sea ice.

Figure 1: components of global warming for the period 1993 to 2003 calculated from IPCC AR4
The percentages were calculated from Figure 5.4 from Section of the IPCC 4th Assessment Report (h/t to Humanity Rules for the heads up). The IPCC graph shows changes in energy content for two different periods: 1961 to 2003 and 1993 to 2003. The ocean heat figure of 93.4% is almost certainly an underestimate as it only includes ocean heat down to 700 metres (Levitus 2005).
(The text for the image(s) on this Web page was taken from the above source.)