Import a bunch of certificates into the correct certificate store using a script
I use CertMgr.exe and a simple bat file to import certs.
certmgr.exe -add -c ca.cer -s -r localMachine root >> log.txt
certmgr.exe -add -c test.cer -s -r localMachine root >> log.txt
certmgr.exe -add -c edu.cer -s -r localMachine root >> log.txt
Here is a TechNet article which documents what commands/usage you can do with certmgr.exe