The available exchange-correlation functional in ATK-DFT includes the LDA and GGA. Actually, both of them are the same level. It is difficult to give a definitized suggestion to say which one of them is much better for the problem under your study. The job for the GGA calculation may somehow slightly heavier than that of the LDA, but usually it can be ignored.
Larger basis set, heavier job and more accurate. In other words, for accuracy: DZP > SZP > SZ; for speed: SZ> SZP> DZP
Only the ballistic transport can be calculated, the diffusive transport cannot be.