Clearance is the same everywhere in Colombia - you hire an agent, they take all your
documentation for a day or so and do stuff with it. The agent then brings immigration and
customs to your
boat and fill out some more paper
work and then you are done. It generally takes 2 days to check in and another day to check out.
There is more to see and do in Cartagena because it is a much larger city. Santa Marta is funky and nice in a different way. Santa Marta also has a large modern marina, if that is of interest to you leaving your
boat. Cartagena does not have a good marina, but you can haul your boat at several yards there instead. Santa Marta is the better stop if you want to hike up the Sierra's and/or visit the
Lost City. Cartagena probably has better/more flight choices out, but you will be connecting in Bogota or Medellin for anything international. The bus ride between the two cities is long ~5-6 hours and you need a taxi to get to the station. There are also shuttle services, but these too are long rides.
To make a blanket statement that Cartagena is terribly hot and humid is uninformed. Yes, if you are from coastal central
California and you visit there in the summer months, it is hot and humid like all tropical
Caribbean places (and pretty much everywhere else in the US also). If you are smart enough to visit in the
winter months, and are experienced with tropical
weather, you will find Cartagena has much more delightful, cooler, drier
weather.
It is doubtful that you will see much of the
interior of Colombia in 2 weeks unless you are a disciple of Chevy Chase's "vacation".
Mark