These measurements depend on knowing what the apparent wind direction is fairly closely, within a couple of degrees is perfection but that is still requires calibration. What I would suggest is that you take a photograph of your masthead fly from directly below it like the one to the left. You need to measure three things. You can measure them directly off a paper printout using a protractor. Alternatively, you can import the photograph into Google SketchUp or Photoshop and use the protractor tools in the programs. I prefer Google SketchUp (free) over Photoshop ($$$), which I also have. You need to measure the angle between the flags. What you will want is half that angle for entry into the tools. You will also need the angle the flags fill and the angle of the fly tail. All these angles are measured from the center of the masthead fly support. You can see the trace lines I used to make the measurements.

You can still use this tool without calibrating and just use my numbers or eyeball what you have. Because you will be using the same masthead fly for determining what course you sail as you did in making the measurement, some of the potential errors cancel. Being off a couple of degrees one way or the other doesn't matter that much. You may also want to make sure that your masthead fly is centered correctly. I will show how I did both of these measurements below using Google SketchUp.

First, take a picture from the stern offset looking up at the masthead fly. On my boat, the masthead fly is offset slightly so I moved my camera away from center by approximately the same distance. You can see the backstay running up the picture from over at the left to the top of the mast.

Next I imported the picture into Google SketchUp (free program) as follows.
1) On a blank page, draw a rectangle. This will be the base for your work.
2) Click File, then Import, then enter the name of your photo and select "Use as Texture".
3) Click on the lower right corner of the rectangle to place your image, then move the cursor to the upper right and click again.
You can now use the SketchUp Protractor tool to make your measurements. It may be helpful to draw lines to the various points you want to measure from the center of the bolt on the masthead fly but that is optional as you can use the protractor directly to make the measurements.

On this picture, what we are interested in is the difference between the two flags as compared to the vertical. In SketchUp, you can place the first point of the protractor in the center of the bolt, then click on the vertical (blue axis) then click move the protractor to each flag reading off the angle. They should be the same.

The second picture you need is from directly under the masthead fly looking straight up. Import it the same way that is described above. In this case you need three measurements.
1) The width of the flags. In this case, 9.5 degrees.
2) The width of the tail. I measure 15 degrees.
3) Half the amount of the angle between the two flags. I measure 55.75 degrees so my flag spacing is 27.875.
It should be noted that I measured a Windex at West Marine and the tail was 15 degrees and the flag 10 degrees. The standard setup is to have the flag spacing at 60 degrees or +- 30 degrees. It doesn't make a significant difference in the calculated target boat speed so feel free to use the standard numbers.