Pageant is not intended for automation.
Even if you try to run it as service, how would you provide a passphrase for the key?
You would have to have the keys unencrypted, but then, there's no point of using Pageant. You can use an unencrypted key directly in the script.
See https://winscp.net/eng/docs/faq_passphrase

Hello
I'd like to find out how i can use Pageant whether user is logged or not.
Cause if i'm logged, Pageant know about private keys and passphrase for keys, but when i logoff and reconnect some time later Pageant know nothing about private keys.