Figuring out how to measure motor height on a bassboat can be a bit confusing at times; hopefully this will help sort out the confusion.
Basically, there are three main ways to measure motor height (that I'm aware of); probably the most common is:

 #1: Height of the motor off the transom
This is simply a measurement taken from the top of the transom (top of the aluminum plate on top of the transom), to the bottom of the motor "brackets".  Look at the part of your motor that would be resting on the transom if you had the motor all the way down on the boat to where the brackets were actually resting on the transom.  You want to measure from the transom to the flat part of this bracket, disregard the downward pointing "hooks" at the front of the bracket.  (Any measurement given as "off the transom" will be to the flat part; if you measure to the bottom of the brackets your motor will be higher.)
If you have a jackplate, you may have to get a bit creative in your measuring; you may have to "extend" the flat part of the bracket forward with a straight edge to where you can then measure up from the transom.

In the photo above, we've measured from the motor bracket to the top of a Detwiler manual jackplate.
As you can see, the measurement is about 2 1/2".

In the second photo, we've measure down from the top of the Detwiler jackplate to a point level with the top of the transom.(Putting a straight edge on the top of the transom to "extend" it out would be more accurate.) This measurement was approximately 4". Add the two measurements and you get 6 1/2".  This was the height of my 225 Yamaha on my TR21 Triton.      

 #2. Propshaft in relation to pad
Take a long straight edge, (long carpenter's level or long steel ruler, etc.), and place it on the bottom of the pad in the center.  Tilt your motor until the bullet of the gearcase is parallel with the straight edge.
Measure from the top of the straight edge to the center of the front of the "bullet" on your lower unit.  This will be the center of the propshaft.  This measurement would be the inches of the propshaft below or above the pad.  (In the case of the faster hulls, such as Allisons, Bullets, Strokers, etc., this measurement could actually have the propshaft above the pad.)

 #3. Pad to bottom of motor brackets
This is a measurement that has been used for BassCats, I'm not sure that it's still used. 
This is somewhat similar to #2, in that you are again measuring with a straight edge from the center of the pad, but this time you're measuring up to the bottom of the motor brackets, (as in #1).
Again, make sure that you are measuring to the flat part of the brackets; disregard the "hooks" at the front of the brackets.
Make sure that you are measuring straight up, at a 90 degree angle to ensure that your measurement is accurate.

Any questions?  If so, send me an e-mail and I'll explain it better, (or point you to someone that can help.)