Just replaced my spark plugs last night and trying to get my 02 SS running good again and I noticed the tubes under the TB. The passenger side one isn't connected to anything and the driver side has a plug on it. I've attached a pic I found online and hopefully I can get some guidance.

 

those are for the coolant to run through. they do not need to be capped. most people just do the " tb bypass mod".

 

Oh that's right! Just got back into an LS1 and learning all over. It does have a bypass mod.