First you need to open the root certificate store...
HCERTSTORE hRootCertStore = CertOpenSystemStore(NULL,"ROOT");
Then add the certificate using one of the CertAdd functions, such as CertAddEncodedCertificateToStore.
CertAddEncodedCertificateToStore(hRootCertStore,X509_ASN_ENCODING | PKCS_7_ASN_ENCODING,pCertData,cbCertData,CERT_STORE_ADD_USE_EXISTING,NULL);
pCertData and cbCertData would likely point to the certificate data that you read from a file (not sure if the certificate will be in a file, or how you will include it in your application).
Then close the store with...
CertCloseStore(hRootCertStore,0);
NOTE: This code if run as the user, installs the certificate to the user's root store, not the computer's. It also results in a warning dialog that the user must understand and select "Yes" to authorize the import. If your setup program can run this code in a system account, the import will affect the computer's root store and not warning dialog will be shown.