Version of header files to use?

I have been trying to get Pixhawk to arm through Matlab serial connection, but to no avail…However, I am now thinking that I might have a mismatch in the versions of Mavlink.

Should I be using the header files from Mavlink version 1.0 or version 2.0? While the Mex code compiles without trouble with version 1.0 header files, I get this error when I try to use version 2.0 header files.

#include “mavlink\include\mavlink\v2.0\common\mavlink.h”
#include “mavlink\include\mavlink\v2.0\mavlink_types.h”

and the compilation errors are
(numerous instances of thie error) documents\matlab\mavlink\include\mavlink\v2.0\mavlink_conversions.h(48) : warning
C4244: ‘=’ : conversion from ‘double’ to ‘float’, possible loss of data

(numerous instances of this error)
documents\matlab\mavlink\include\mavlink\v2.0\common./mavlink_msg_heartbeat.h(5) :
error C2146: syntax error : missing ‘;’ before identifier ‘__mavlink_heartbeat_t’

I would truly appreciate any help/directions/pointers to address the problem…