We are considered seporate as we have our own bylaws and bank accounts and the money we fundraise is our own the only money central collects is systemwide dues so each family only pays once no matter how many kids you have in different schools these funds are then used for the PTO scholarships given out. thats it. The central does not tell us how to run or have any control over our actions. I don't know if this helps make this clearer. but I guess it sounds most like what Tim said.
I think the better analogy is the relationshiop of a local PTA to its state PTA. In most states the local PTA is granted 501(c)(3) status under the umbrella of the state PTA. But the local PTA is still a separate legal entity and the local PTA is still certainly eligible for grants, etc.
More and more PTO groups are doing this, where they group together as a townwide for the 501(c)(3) purposes (and other communal benfits). It's a nice option, can save on fees and paperwork, while allowing a group to remain independent.
It's not clear from your post if your group is a separate legal entity from Central PTO. If your Central PTO is filing the Form 990 each year, it sounds to me like your school's group is a committee of Central PTO, not a separate entity. I also suspect that means Central PTO is the 501(c)(3) organization, not your PTO on its own. This structure works fine, but may complicate your grant a little.
As Mum24 said, if your PTO is a committee of the one centralized 501(c)(3) organization, it seems a grant would be made payable to Central since they "own" the non-profit status. Maybe you could work a deal with Central to designate the grant money for your school, but you may not have any real control over that. I may be jumping to conclusions of how your group is structured, but if my assumption is correct, this might be an example of a disadvantage of one centralized group organization.
Depends how you are set up. Even though you get your tax exempt status from "Central PTO," are you still a separate legal entity with your own tax ID number? So you're sort of a chapter of the Central PTO? If so, should be easy--just fill out the grant application with your PTO's name and tax ID number, with the appropriate documentation from the IRS (assuming the grantor requested that).
If you're not separate, you can try to do the grant application as a separate school, but the grantor is likely to make the check out to "Central PTO," and you might have a hard time getting it allocated to you. Seems to me, though, that if your run it through whoever the powers that be are at the Central PTO level, it shouldn't be a problem.
We are in a different situation with a Central PTO filing taxes for all our schools together and we are a 501c3 through the Central PTO. My question is we would like to apply for a grant for just our school can we do this, the grant says you have to be 501c3.