I am going to take the airbox off of my 99 elantra and replace it with a custom air filter. I will purchase a new SR intake in a few weeks, my question is... There is a sensor of some sort when facing the air box on the left side towards the bottom. What do I do with it?

LiVE

 

That is the flowmeter..
Either strap it on the filter or make a small hole on your oem tube and strap it there.Use some silicone in both cases for better result.You can leave it hanging outside if you like but i wouldnt do that.No CEL if you leave it hanging and no worries about damage.
If you are gonna buy the sr cai very soon leave it hanging outside no prob.

 

That is your air temp sensor and its not a good idea to let it just hang there. It should be placed inside the intake before the MAF and it should be secure and not bouncing around in the intake cause they are kinda fragile. Your best bet would be to drill a hole somewhere in your intake tube so the factory gromet can be placed in with the sensor.

 

Both Angelos and MAXTIB are correct.

There is a MAF sensor (the black tube with the wire connection on it) that you need to keep, and the Intake Air Temp sensor (IAT) that you need to keep in the intake air stream.

you need to drill ahole in your intake tube for the IAT to keep it in the intake air stream.

You may be tempted to cut the grilling off the MAF. DO NOT DO THIS. Trust me, from experience, it leads to very erratic MAF readings and a poor running engine.