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".