Pageant can automatically load one or more private keys when it starts up, if you provide them on the Pageant command line. Your command line might then look like:
C:\PuTTY\pageant.exe d:\main.ppk d:\secondary.ppk
If the keys are stored encrypted, Pageant will request the passphrases on startup.
If Pageant is already running, this syntax loads keys into the existing Pageant.