Huh, can't believe there weren't any replies.
University of Houston Main Campus and University of Houston - Downtown are considered two separate universities (similar to the UT school system), meaning you'll have to request transcript transfers between the two.
University of Houston - Downtown is a lot smaller than University of Houston Main Campus.
UHD mainly serves undergraduates and offer 4-year degrees. They're starting to expand into higher level education, but mainly, it's for undergraduates. UH though serves three times the number of people and offer a lot more bachelor's and master's degrees as well as a handful of post-doctoral degrees. UHD is comprised of five buildings (though most of the classes are situated in one). UH has a heck of a lot more and is big enough to require a shuttle bus system and service whereas UHD is not.