Angles

That is pretty much the reason why the different options exist. When you first place the angle object you may find that its default configuration is not measuring what you expect, because of the ambiguity around which leg is the base leg and in which direction the angle is measured. So these options let you tell the program how the angle should be measured.

The dashed leg is always the base leg from which the angle is measured, in other words the angle is the one that spans from the dashed leg to the other one. In the latest version I added a small arrow to make this clearer.

The default direction is counter-clockwise as in trigonometry, but depending on whether the person is facing left or right you will need to change this. It's just a default.

Since we rarely measure angles above 180° when measuring human range of motion the default is "signed" which means any angle between 180 and 360° is converted to be in the 0 to -180° range instead. So let's say your anatomical reference position has 0° as the full extension, but that person has hyper extension and can actually go further, bending the joint backwards, then it would measure as negative, maybe -5°, instead of measuring 355° which wouldn't really make sense in this context. But it's an option for when it might make sense.

For measuring joints range of motion it's probably better to use the goniometer and set the reference axis.

The first measurements you need to figure what configuration corresponds to what makes sense compared to what you know the value should look like when you progress from flexion to extension or vice versa. This is similar to what you would do with a physical goniometer, you place it as you know it should be placed but then you check that the measured value makes sense because it's easy to mix things up. There is no way the program can know in advance in which direction the motion goes or how you want to measure it.