The USB port on the side is for future updates, it will currently do nothing if you plug it into your computer. Also, the servo polarity is labeled ontop of the programmer, the polarity on all of the ports is the same.
As for the servo issue, make sure your linkage geometries are identical, if one linkage is even slightly out it will cause one servo to have to move farther or shorter than the other servo which can cause all sorts of speed sync problems.
The manual was kept short and basic because the number of things the programmer can do wouldn't be able to fit into a manual small enough to put inside the box with the programmer.