Acrobat/Reader on Windows uses Windows Trusted Certificates by default. If you want to have them in Acrobat's trusted store as well, you can export them from the Windows store (public key only) and then import the exported .cer files into the Acrobat's trusted certificates store.
I have tried something similar by trying to import the Windows Cert Store into Adobe, but I never did have it work. I just recently found the option is XI for Adobe to look at the Windows store itself.
XI: Edit > Preferences > Signature > (Verification) More... > (Windows Integration) Check Validating Signatures, Check validating Certified Documents
It should happen right away; although I will note I am having issues with this working for Non-Admins on a Terminal Server. Might be a privilege issue.
If you want to set via GPO:
Key Path: Software\Adobe\Adobe Acrobat\11.0\Security\cASPKI\cMSCAPI_DirectoryProvider
Value Name: iMSStoreTrusted
Value Type: Reg_DWORD
Value Data: 62, or 60 (Hex)
Link: Digital Signatures