I'm sure schools take all your GPA's into consideration but.......
I don't think your science GPA matters too much esp. since you took many hard science courses that are going to be unrelated to PT (schools know this.) Like for example I did bad in organic chemistry and during one of my interviews the interviewer was like what is this D, oh organic chem we do not require that (basically she was like who cares about that, and moved on to ask about other things).
Also, most PT schools don't have a minimum overall science GPA that is required to apply, so that isn't going to make it so that you can't apply to schools.
Your cumulative undergrad and cumulative total GPA matter (some schools have minimums of 3.0 or 3.2) , and the most important part is your prereq GPA, almost all schools have some sort of minimum you need to apply.
As long as you meet the minimum requirements to apply to a school, do it! Your chances might be lower, but if you have an okay prereq GPA, good GRE score, good recommendation letters, and a good essay then you will at least be considered!
You might want to apply to some private schools or some schools in your state since many state schools accept like 80% in state students, so I wouldn't apply to an in-state school in a state I don't live in that has stats like that. Also, there is a thread on schools whose average GPA acceptance rates are the lowest. Haha! But in general you never know, so you might as well go for it. I wouldn't advise applying to over like 10ish schools though bc it is expensive and PTCAS has stats that say your chance to get into a PT school doesn't change once you apply to more than like 7 schools. Apply to ones you are interested in bc there is no way you are actually excited about 20 schools and it is expensive!
Anyway, I had a low GPA, applied to 12 schools, and I'm on 5 waitlists. So no I havn't gotten in anywhere, but I think it is worth a shot & in the mean time try to get your prereq GPA up and do good on the GRE for if you have to apply next round. I know it is hard to get your overall GPA up when you have so many credits into it already but I do think you have a chance.