Right now I've got a aftermarket header that has a o2 bung which is plugged. Then I got the downpipe, midpipe with the primary sensor attached, 2nd o2 sensor about 6 inches from the primary, glasspack instead of a cat, and a cat back with muffler. I don't have any issues with a CEL but was wondering if moving the primary up on to the header would be beneficial in any way.

 

Not likely to change anything unless you have an exhaust leak at the flange, but you haven't described anything about the car. What chassis/engine/ecu? Are you talking about a wideband/lambda sensor, or a narrowband sensor? Why do you have two sensors if you don't have a catalyst?

 

Here's them deets
97 accord 2.2 vroomtec with a stock ECU
I'm using the OEM O2 sensors and I'm pretty sure the primary is a 4 wire. That's all I know about them. As far as why I've got the secondary on there is because I don't have a tune with 02 sensor bypass, don't want a CEL for a missing sensor, and I think it would make it run too rich or too lean.
I've just got a o2 sensor fouler on that 2nd one and it keeps the CEL from going on.
My priceless eBay header came with a bung right on it, so I was curious if I was supposed to move the primary to the header.

 

Yup, nothing worth expending brainwaves over then.

FWIW, secondary sensors have nothing to do with the mixture. Only there to monitor the catalyst. It may or may not throw a code, even with the non fouler on there. Only time will tell.

The header came that way because some years/trims came with the bund on the A-pipe, some years came with the bung on the front of the catalyst, as you have. It makes no difference what location you choose to use. The ecu can only determine rich or lean with a narrowband (not by how much) and doesn't trim at WOT anyway.