One better flight search engine than Kayak appears to be Taca Airlines (albeit based in the UK). For BOG -> CTG -> PTY -> BZE -> SFO, as of June 2nd 2014, Kayak's cheapest flight is $1790, while Taca's is $1630.
Copa, despite being local, fared far worse than Kayak on a BOG -> PTY -> SFO route ($1256 vs. $1088). Its interface is also as clunky as Avianca's, in that it doesn't list the prices of the many options it comes up with, nor does it list the total time per leg (you have to do mental math, with time zones thrown in for fun), and you can't easily modify a query.
Also, beware that Kayak may fail when you search for more than 4 legs: I was looking for a 4-leg multi-city combination in the Caribbeans, and Kayak found nothing:
BOG -> CTG
CTG -> PTY
PTY -> BZE
BZE -> SFO
But when removing the last leg and searching for it separately, Kayak found flights amounting to 27% less than ITA's best price.