PTCAS will calculate a wide variety of GPAs for you, all of which are either self-explanatory or described in the instructions/FAQ. It is all done based on what category you assign each class to. Your PTCAS pre-req GPA can and probably will vary (sometimes substantially) from the pre-req GPA you have at a given school. PTCAS generates a "core pre-requisite" GPA based on the one class you assign to each "core pre-requisite" designation. Essentially every PT school is going to require a year of A&P, a year of gen chem, a year of physics and a stats class. All require at least one psych class and the vast majority require 2. The variation will usually come from whether or not a school has a year of biology or ex. sci./kinesio as a pre-req, and if each school considers other things (eg. humanities, English, things you had to take to take to graduate college) to be pre-reqs, or if they just have an oddball class that most schools don't have (eg. nutrition, medical terminology, etc) as a pre-req.
The easiest thing to do for yourself if to just put all your grades in a spreadsheet: column A is the class, column B is the grade, column C is the number of credits column D is the PTCAS value (eg. 4.0 for A+/A, 3.7 for A-, 3.3 for B+, etc), column E is C times D to get quality points. You then divide the sum of column E by the sum of column C and you've got your PTCAS cumulative GPA. Do the calculation by cherry-picking out the classes of interest (eg pre-reqs) to get any other desired GPAs.