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1. In the process of replacing the air filter I noticed that in the past someone has overtightened the 6 bolts and now they are stuck (they just spin). Is it best to replace the whole air box? Is so, where do I buy it? Suggestions.

2. What is the box upstream of the air filter left of the engine? If I replace the filter with something aftermarket, do I remove it also?

Thanks in advance.

 
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You could drill the 6 bolts out on the original and replace them with hex bolts and nuts. If that's possible on your set up.

The box upstream from you air box could be another air box. Personally in my Civic, I have an air box right in the fender, and another right in front of my battery which then leads t the throttle body. And as for going aftermarket (ex. cold air intake) yes, you'd most likely remove both.

 
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its easier to just replace the airbox and next time only tighten them with a screwdriver (hand tight) and not a socket wrench. the box without the filter is a resonator, kinda like a muffler for the intake to make it quiet. aftermarket intakes replace all the plastic pieces.

 
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aftermarket intakes on 7th gens replace everything from the throttlebody including both air boxes and everything with them. if you want to see a picture, just use the search and type 'intake' and look for any thread that has a picture attached.

if you want to stay stock and just replace the airbox, im sure there is someone on here that you can pick up a stock setup from (most people here have intakes anyway) or you can get it from a local yard, but if it was me, i would just do what slammedzcatch said and drill the existing stripped bolts out and use a regular long bolt that slides into place with a nut on the other end.

 
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Agree with the above. Before I owned the car, someone overtightened. They are not bolts but just screws. But like you said, on the new one I will just use a screwdriver and just get is snug.

After my question I went to the AEM site and they had instructions to replace stock air intake and they also called it a resonator and had some good pics.

Ultimately, I am going to try and find a cheap direct replacement before looking at the aftermarket option. Thanks for all the input everyone.

 
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I always kept mine lubed to prevent them from sticking.

The bottom of the threaded inserts are open and exposed.