We have carried out high-resolution observations along one-dimensional cuts through the three Galactic super-shells GS 064-01-97, GS 090-28-17, and GS 174+02-64 in the HI 21 cm and CO J=l-0 lines. By comparing the HI data with IRAS data, we have derived the distributions of the $I_{100}$ and $T_{100}$ excesses, which are, respectively, the 100 ${mu}m$ intensity and 100 ${mu}m$ optical depth in excess of what would be expected from HI emission. We have found that both the $I_{100}$ and $T_{100}$ excesses have good correlations with the CO integrated intensity W co in all three supershells. But the $I_{100}$ excess appears to underestimate $H_2$ column density N($H_2$) by factors of 1.5-3.8. This factor is the ratio of atomic to molecular infrared emissivities, and we show that it can be roughly determined from the HI and IRAS data. By comparing the $T_{100}$ excess with $W_{co}$, we derive the conversion factor X $equiv$ N ($H_2$) /$W_{co}{simeq}$ 0.26 - 0.66 in the three supershells. In GS 090- 28-17, which is a very diffuse shell, our result suggests that the region with N($H_2$) $le$ $3 { imes} 10^{20} cm^{-2}$ does not have observable CO emission, which appears to be consistent with previous results indicating that diffuse molecular gas is not observable in CO. Our results show that the molecular gas has a 60/100 ${mu}m$ color temperature $T_d$ lower than the atomic gas. The low value of $T_d$ might be due either to the low equilibrium temperature or to the lower abundance of small grains, or a combination of both.