Roofing, Gutters and Waterproofing - Exposed nail holes in roof vent

Hello,

I am repairing a small section of my three-tab composite roof, and installing a roof vent for my bathroom fan. (it is the type of roof vent that the fan hose connects to).

What is puzzling me is that in addition to the two holes at the top of the roof vent (which will be covered by the top course of shingles), there are also two holes at the bottom of the roof vent.

If I put nails into these holes, they will be exposed, which is something I thought should be avoided

Here is a picture of the roof vent:

http://jonnycats.home.comcast.net/~jonnycats/RoofVent.jpg

I'm hoping that the people who make the roof vent know what they are doing, but what exactly am I supposed to do here?

Am I supposed to run the lower course of shingles to where they are butting into the left and right hand side of the section of the vent that rises up from the bottom plate, so that the nail/nail holes are covered by them?

In other words, should the shingles (represented by the mustard colored overlay) cover the flange as in this picture?:

http://jonnycats.home.comcast.net/~jonnycats/RoofVent03.jpg

In all of the other roof vents that I have seen, the entire width of the bottom end of the vent flange is treated like a shingle, and is just left exposed without any holes or exposed nails, which is why this configuration is puzzling me.
Thanks for any help on this.

The nail holes will be exposed, and only a daub of Henry's roofing cement will be required to seal the heads if that makes you feel better. For the most part they will self seal once they are driven into the shingles below. I like to put a little cement over the heads anyway. You only will run the shingle over the top of the vent. The vent itself will act as a shingle and shed water downwardly without restriction.