Just to give another perspective, I'll tell you how I do it.  I am aligning them the same way I use my Boeing 737-900 ERX.

First I bring up the 2d IRS from with the quick selection tool that CptSim provides (Shift+3), then I bring up the 2d FMC/CDU using the same tool.
I place one next to the other and I go to the PPOS page of the CDU and copy past the LAST POS to the scratch pad.
Then I switch the knobs on the IRS past ALIGN to NAV which will bring up boxes on the CDU and I move the present position from the scratch pad to the boxes.  The IRS will align and when it is I will move the top knob on the IRS so the Long/Lat will show on the display of the IRS.