The cloud screening procedures for the two products use similar principles but different tests due in part to different bands used in the retrieval algorithms and different pixel resolutions used in algorithms. Really 'cloud mask' is not 100% correct as a term, they are more like a 'suitable pixel mask', and both algorithms have different requirements for pixel type (e.g. Dark Target has a surface brightness criterion).
Dark Target and Deep Blue quality assurance tests and definitions are independent and unrelated, and it is coincidental that they use the same (0-3) scale. Follow individual group recommendations for their products, or better yet, use only the prefiltered scientific data sets (SDSs).
One reason is that AOD is normally low in these areas so AOD variability is similar in size to the retrieval error. Another reason is that these areas may have bright surfaces and/or atypically colored soils which the two products will retrieve differently.
The merged product is a single SDS (AOD_550_Dark_Target_Deep_Blue_Combined) comprised of only high quality dark target (QA=3 over land, QA > 0 over ocean) and deep blue (QA 2 & 3) data to produce a global 10 Km product. Over ocean this product uses only dark target retrievals. Over land, monthly NDVI maps are used to assign which retrieval will fill the merged SDS. Over bright surfaces (NDVI < 0.2) the deep blue value is selected. Over dark vegetated surfaces (NDVI > 0.3) the dark target value is selected.
For advanced users it is best to know the details of the validation of each product and the locations and seasons where each product has the best performance. Additional information can be found here: http://onlinelibrary.wiley.com/doi/10.1002/2014JD022453/abstract
This is a big question and we can only provide very general answers in this FAQ format.
Dark target has separate algorithms for land and ocean. Deep blue in the MODIS aerosol products is a land retrieval only. All total column aerosol retrieval algorithms must account for and remove the surface reflectance signal to accurately determine the aerosol signal. Dark target and deep blue retrievals have different ways of accounting for the reflectance signal coming from the land surface.