The purpose of the second hole is an auxillary drain.  Either plug it or install a trap and drain like hte other one.  Your primary drain is plugged.  Blow it out or remove and flush with garden hose.  DO NOT put a lip lock on it, however, as condensate drains can harbor Legionairs Disease (Legionella bacteria).

Algae tabs are great but bleach is corrosive.  Use at your own (considerable) risk!!

Funny drain stories #37:

Didn't see this one myself (thankfully) but has been confirmed by all the guilty parties.

Used to be a drain cleaning gadget that used a can of high pressure gas.  When you stood on the thing, it puctured the can and dumped the contents all at once - couldn't stop it.

House had two bathrooms and sewer was REALLY plugged up.  Tried once to clear it and had no luck.  Went on roof and capped vent, plugged lavatories and tubs.  Had one comode off floor and used that as entry point for gas canister.  Stood on can and got a satisfying whoosh as water was forced down line.  Seconds later came this blood curdling scream from the lady of the house, followed by "oh my GOD"!!  Yep, forgot to plug other commode.  ENTIRE bathroom was covered in shit.  Shit stalagmites as it were.  Great gobs of runny dripping shit - everywhere.

Use a bit of caution when blowing out drains!

A trap ondrains and plumbing fixtures is required by code to prevent sewer gas from backing up and being released in the living space.  Sewer gas stinks, is unhealthful and is explosive.

Condensate drains from AC units are not allowed to be connected to sewers in most jurisdictions, hence no trap is required by plumbing codes.

A trap on an AC serves two purposes, though neither is related to sewer gas.  One is to prevent leakage of air either into or out of the duct system.  Two is to allow the condensate to drain out.  If the drain is on the suction side of the fan and air is "pulled" through the coil a negative pressure exists at the drain and will prevent the water from leaving.  A trap of adequate height to exceed that negative pressure stops airflow equalizes the pressure differential and gravity allows the water to continuously run out.  This can be clearly seen on some units - remove the drain line and nothing runs out; install a proper trap (pre-filled with water) and a large steady stream of water comes out!  Remove the trap and it stops.

Your "funky smell" is algae growth on the evaporator coil and/or in the condensate drain pan (assuming some moron has not connected the drain to a sewer or floor drain).  Have the coil cleaned, check the drain and add algae growth control tablets to the drain pan.  A pull through coil with no trap will suck in air.  If that air is from a dank basement or contains sewer gas or nasty air from a wet crawl space you get a "funky smell" in the house.

The "auxillary drain" hole in an evaporator is an air leak allowing air or smell in, conditioned air out.  Plug it.

TRW, yes they have a drain.  According to code there should also be another auxillary pan under the unit.  In well planned installations there is a float device in the aux pan that turns off the condensing unit and/or turns on an alarm light when water gets in the aux pan (it never should).

The aux pan drain requires no trap.  The unit drain does.  Often in an attic install the second drain port on the airhandler is used as well for a total of three.  (Two trapped, one not.)

Different installers route the drains to different places.  I prefer they discharge in a visible area and be labeled as #1, #2, #3.  1 is OK (primary drain), 2 is a warning (aux AH drain), 3 (AUX pan drain) is impending disaster, shutdown at once!