The fort seem to be custom built to provide protection against sea attacks. You can see holes in port walls, built at various positions and angles, through with either cannons could be fired at enemey ships or hot oil can be poured against enemy soldiers trying to climp up against the port walls. Excellent defense strategy of those times, when air attacks were unknown...
There's no remains of any palace on the port- Quite a small area indeed for a palace. Just few constructions and gardens remain, with a temple below.
How to go to Bekal Fort?
If train timings are convenient go by train. Bekal station is very near to Bekal fort- you can probably walk or hire an auto.
Mangalore Airport is the nearest one. Adequate road transport is available from Kasargod and other towns in Kerala along NH 17.
How much time to spend at Bekal Fort?
You can walk around the port in few hours time-Add some more time to relax near sea shore and you can make it a half day program.
Carry an umbrella- there are not many places where you can take shelter if it rains.
Hundreds of movies have been shot at Bekal Fort, Manirathnam's Bombay was most significant one I guess.