CatnPhx, we registered our D to take the SAT through the Midwest Academic Talent Search. But to make sure she would be eligible for CTY classes and perks, we also enrolled her through CTY. I believe we did pay two fees to do this. Here is an email we got when I asked CTY about it (back in 2007):
"Thank you for contacting us. Students who test through a different program can
fax a copy of eligible test scores to CTY (fax: 410-735-6105) when they are
ready to participate in one of our programs. You do not have to apply to both
programs. However, you may want to view how we are assign Summer Program
courses here (CTY: Intensive Studies for 7th Graders and Above
you enroll her into both the MATS program and CTY Talent Search, she would only
need to test once. The CTY Talent Search fee authorizes a student to test in
one academic year and only needs to be resubmitted if students wish to test in
the next academic year. Otherwise, a student will always be considered a
previous talent search participant."
This email implies that you have some priority in the enrollment process if you are a CTY participant when you actually take the test. I don't think she would have gotten the Cogito (online forum) invitation from CTY if we had not enrolled her through them (which we did prior to her taking the test). That alone was worth the fee, although she never did attend CTY. As I said before, her scores got her into Davidson THINK, though.
I'm sorry I can't really remember more details about this registration process. In 2007, you couldn't just send the scores to those programs like you could to a college (but maybe you can now, I don't know). If I were you I would call the programs you are most interested in and ask them about this. Before you register your D for the test, as you will want to register her through one of their programs and pay their fee for it, I think, to get maximum benefit from the program.