Shortening Pant Pattern??

Please forgive my novice-ship of sewing, but I am JUST getting into using patterns...LOL
I am making a simple pair of PJ pants and I realized as I was pinning the pattern to my material, that half way down the leg it has a line that says shorten or lengthen here. So, according to my calculations, I need to shorten it up at least 3 inches for the finished product to be short enough to meet my feet..LOL If that makes any sense.
I like my britches to be just a little longer than my ankles.
Anyway....My dilemma is...I assume I draw up and fold the lower portion of the pattern and pin (or tape) onto the upper portion at the line provided, BUT...I see that the lower cutting lines become out of alignment with the upper cutting lines and am baffled how to do this correctly.
Again, I am sorry for what I am sure is a simple thing, but I have never made pants with a pattern before and don't want to waste the material, etc.....!
Thank you.
Vicki

By the way...
The pattern I am using is:
http://mccallpattern.mccall.com/m5534-products-8083.php?page_id=907

That's right. You can tape in an extra piece of paper and draw in a line to smooth the edge.

Make sure you are allowing for the hem? PJ patterns often have deep hems.

Good luck!

Thank you...
I opted to just cut as is and hem in the normal way! I saw that there wasn't that much difference in the tapering down the leg, so it worked out for me in the long run.
This was just a practice sew, to get back into the swing of sewing and trying out my new sewing and serger machines..
Thank you for your reply.