How do I align the IRS?

Here's the basic method:

1. Move the IRS selectors from OFF to NAV
2. Open the FMC and go to the POS INIT page, downselect the GPS Position into the ENTER IRS POS prompt (LSK 6R).
3. Wait the specified time (set in the PMDG/General/IRS dialog) - a countdown is visible in the upper left corner of the ND.
4. IRS alignment is complete when you have a full PFD and ND displayed.

If you see the ENTER IRS POS prompt twice

This is a feature of the real aircraft's IRS and happens because the plane has been moved from the IRS's last known position while the gyros were powered down. In FS this can happen easily if you start your next flight after a shutdown from a new airport or gate location. The FMC will ask for the current position twice just to make absolutely sure that it's accurate.