To import a certificate using SCCM, use certutil in either PowerShell or a bat file. Create an application of all your certs and use a script to import them. For the detection method, you will find the certificates at:
Under each store will be a Certificates key containing the certs in a GUID form. This GUID will be same for a certificate on every computer. You can use a registry detection method to detect if your certificate is present. To find which certificate is added, just compare the GUIDs before and after import.